HEADER SIGNALING PROTEIN 14-SEP-15 5DQ0 TITLE STRUCTURE OF HUMAN NEUROPILIN-2 B1 DOMAIN WITH NOVEL AND UNIQUE ZINC TITLE 2 BINDING SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUROPILIN-2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: B1 DOMAIN, UNP RESIDUES 475-430; COMPND 5 SYNONYM: VASCULAR ENDOTHELIAL CELL GROWTH FACTOR 165 RECEPTOR 2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: NRP2, VEGF165R2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B-TEV KEYWDS NEUROPILIN, VEGF, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.I.TSAI,R.R.RANA,I.ZACHARY,S.DJORDJEVIC REVDAT 2 10-JAN-24 5DQ0 1 JRNL LINK REVDAT 1 28-SEP-16 5DQ0 0 JRNL AUTH Y.I.TSAI,P.FRANKEL,R.R.RANA,C.FOTINOU,T.S.YELLAND,I.ZACHARY, JRNL AUTH 2 S.DJORDJEVIC JRNL TITL STRUCTURE OF HUMAN NEUROPILIN-2 B1 DOMAIN WITH NOVEL AND JRNL TITL 2 UNIQUE ZINC BINDING SITE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0131 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.13 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 21563 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1161 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1581 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.76 REMARK 3 BIN R VALUE (WORKING SET) : 0.2400 REMARK 3 BIN FREE R VALUE SET COUNT : 81 REMARK 3 BIN FREE R VALUE : 0.2980 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1250 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 138 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.10000 REMARK 3 B22 (A**2) : 0.35000 REMARK 3 B33 (A**2) : -0.24000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.099 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.104 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.067 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.184 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1357 ; 0.016 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1265 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1842 ; 1.753 ; 1.946 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2901 ; 1.015 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 167 ; 7.535 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 68 ;36.685 ;23.382 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 228 ;14.134 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;19.763 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 196 ; 0.105 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1572 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 339 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 656 ; 1.869 ; 2.210 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 655 ; 1.862 ; 2.207 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 827 ; 2.492 ; 3.296 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 828 ; 2.491 ; 3.300 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 701 ; 2.791 ; 2.675 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 701 ; 2.792 ; 2.675 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1016 ; 4.337 ; 3.861 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1568 ; 7.734 ;19.737 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1569 ; 7.733 ;19.785 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5DQ0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-SEP-15. REMARK 100 THE DEPOSITION ID IS D_1000213411. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 291 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.873 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22736 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 36.130 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.23000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 2QQJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25 % PEG 550 MME, 0.1 M MES PH 6.5, REMARK 280 0.01 M ZNSO4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.87500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 22.87500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 49.69500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 52.63500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 49.69500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 52.63500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 22.87500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 49.69500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 52.63500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 22.87500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 49.69500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 52.63500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -90.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 272 REMARK 465 HIS A 273 REMARK 465 MET A 274 REMARK 465 PHE A 275 REMARK 465 GLN A 276 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 278 25.10 -141.78 REMARK 500 ASN A 316 -136.08 50.47 REMARK 500 ARG A 334 -34.63 77.75 REMARK 500 GLN A 353 11.88 57.66 REMARK 500 ALA A 386 -120.60 -122.05 REMARK 500 SER A 416 -47.95 74.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 284 OE2 REMARK 620 2 HIS A 312 ND1 118.0 REMARK 620 3 HIS A 415 NE2 107.5 13.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 362 NZ REMARK 620 2 GLU A 370 OE1 113.7 REMARK 620 3 GLU A 370 OE1 114.5 1.7 REMARK 620 4 GLU A 370 OE2 115.5 5.0 6.2 REMARK 620 5 HIS A 381 ND1 124.6 52.5 50.8 55.9 REMARK 620 6 HOH A 718 O 119.7 6.7 5.4 8.6 47.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 375 OH REMARK 620 2 HIS A 377 NE2 116.3 REMARK 620 3 HIS A 399 ND1 95.9 105.2 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MES A 508 DBREF 5DQ0 A 275 430 UNP O60462 NRP2_HUMAN 275 430 SEQADV 5DQ0 GLY A 272 UNP O60462 EXPRESSION TAG SEQADV 5DQ0 HIS A 273 UNP O60462 EXPRESSION TAG SEQADV 5DQ0 MET A 274 UNP O60462 EXPRESSION TAG SEQADV 5DQ0 SER A 431 UNP O60462 EXPRESSION TAG SEQADV 5DQ0 GLY A 432 UNP O60462 EXPRESSION TAG SEQADV 5DQ0 SER A 433 UNP O60462 EXPRESSION TAG SEQRES 1 A 162 GLY HIS MET PHE GLN CYS ASN VAL PRO LEU GLY MET GLU SEQRES 2 A 162 SER GLY ARG ILE ALA ASN GLU GLN ILE SER ALA SER SER SEQRES 3 A 162 THR TYR SER ASP GLY ARG TRP THR PRO GLN GLN SER ARG SEQRES 4 A 162 LEU HIS GLY ASP ASP ASN GLY TRP THR PRO ASN LEU ASP SEQRES 5 A 162 SER ASN LYS GLU TYR LEU GLN VAL ASP LEU ARG PHE LEU SEQRES 6 A 162 THR MET LEU THR ALA ILE ALA THR GLN GLY ALA ILE SER SEQRES 7 A 162 ARG GLU THR GLN ASN GLY TYR TYR VAL LYS SER TYR LYS SEQRES 8 A 162 LEU GLU VAL SER THR ASN GLY GLU ASP TRP MET VAL TYR SEQRES 9 A 162 ARG HIS GLY LYS ASN HIS LYS VAL PHE GLN ALA ASN ASN SEQRES 10 A 162 ASP ALA THR GLU VAL VAL LEU ASN LYS LEU HIS ALA PRO SEQRES 11 A 162 LEU LEU THR ARG PHE VAL ARG ILE ARG PRO GLN THR TRP SEQRES 12 A 162 HIS SER GLY ILE ALA LEU ARG LEU GLU LEU PHE GLY CYS SEQRES 13 A 162 ARG VAL THR SER GLY SER HET ZN A 501 1 HET ZN A 502 1 HET ZN A 503 1 HET CL A 504 1 HET CL A 505 1 HET EDO A 506 4 HET EDO A 507 4 HET MES A 508 12 HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ZN 3(ZN 2+) FORMUL 5 CL 2(CL 1-) FORMUL 7 EDO 2(C2 H6 O2) FORMUL 9 MES C6 H13 N O4 S FORMUL 10 HOH *138(H2 O) HELIX 1 AA1 ALA A 289 GLU A 291 5 3 HELIX 2 AA2 THR A 305 SER A 309 5 5 SHEET 1 A 4 ILE A 293 ALA A 295 0 SHEET 2 A 4 LEU A 329 ASP A 332 -1 SHEET 3 A 4 PHE A 406 PRO A 411 -1 SHEET 4 A 4 TYR A 361 SER A 366 -1 SHEET 1 B 3 LEU A 402 THR A 404 0 SHEET 2 B 3 THR A 337 GLN A 345 -1 SHEET 3 B 3 ARG A 421 ARG A 428 -1 SHEET 1 C 2 ALA A 341 THR A 344 0 SHEET 2 C 2 VAL A 394 LYS A 397 -1 SHEET 1 D 2 TYR A 357 SER A 360 0 SHEET 2 D 2 THR A 413 HIS A 415 -1 SSBOND 1 CYS A 277 CYS A 427 1555 1555 2.06 SSBOND 2 MET A 338 MET A 338 1555 3654 2.06 LINK OE2 GLU A 284 ZN ZN A 502 1555 1555 1.88 LINK ND1 HIS A 312 ZN ZN A 502 1555 1555 2.18 LINK NZ LYS A 362 ZN ZN A 503 1555 4555 1.92 LINK OE1AGLU A 370 ZN ZN A 503 1555 1555 2.28 LINK OE1BGLU A 370 ZN ZN A 503 1555 1555 2.21 LINK OE2AGLU A 370 ZN ZN A 503 1555 1555 2.67 LINK OH TYR A 375 ZN ZN A 501 1555 1555 1.92 LINK NE2 HIS A 377 ZN ZN A 501 1555 1555 2.12 LINK ND1 HIS A 381 ZN ZN A 503 1555 4555 1.92 LINK ND1 HIS A 399 ZN ZN A 501 1555 1555 2.09 LINK NE2 HIS A 415 ZN ZN A 502 1555 6555 2.18 LINK ZN ZN A 503 O HOH A 718 1555 1555 2.28 SITE 1 AC1 4 TYR A 375 HIS A 377 HIS A 399 CL A 505 SITE 1 AC2 4 GLU A 284 HIS A 312 HIS A 415 CL A 504 SITE 1 AC3 4 LYS A 362 GLU A 370 HIS A 381 HOH A 718 SITE 1 AC4 4 GLU A 284 HIS A 312 HIS A 415 ZN A 502 SITE 1 AC5 5 TYR A 375 HIS A 377 LEU A 398 HIS A 399 SITE 2 AC5 5 ZN A 501 SITE 1 AC6 1 HIS A 399 SITE 1 AC7 4 HIS A 377 LYS A 382 HOH A 602 HOH A 603 SITE 1 AC8 6 TRP A 304 SER A 349 THR A 352 ASN A 354 SITE 2 AC8 6 TYR A 356 HOH A 614 CRYST1 99.390 105.270 45.750 90.00 90.00 90.00 C 2 2 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.010061 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009499 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021858 0.00000