Uniprot accession / id : Q9JKF6  OR   Uniprot accession / id : Q15223
 
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Entry Information
Entry status  (1)
REL
(8)
 
Experimental methods  (2)
X-ray diffraction
(7)
Solution NMR
(1)
 
Authors  (46)
Gao GF
(3)
Lu G
(3)
Qi J
(3)
Yan J
(3)
Zhang N
(3)
Fan Z
(2)
Guo Z
(2)
Shi Y
(2)
Suzuki M
(2)
Wang J
(2)
Ahlsen G
(1)
Bhargava AK
(1)
Brasch J
(1)
Carfi A
(1)
Chen Z
(1)
Clausen O
(1)
Cohen GH
(1)
Di Giovine P
(1)
Eisenberg RJ
(1)
Harrison OJ
(1)
Hong S
(1)
Honig B
(1)
Iwasaki K
(1)
Jin X
(1)
Katsamba PS
(1)
Kawai K
(1)
Krummenacher C
(1)
Li Y
(1)
Lou H
(1)
Luftig MA
(1)
Miyazaki N
(1)
Nakagawa A
(1)
Narita H
(1)
Poulsen FM
(1)
Sakisaka T
(1)
Sangawa T
(1)
Settembre EC
(1)
Shapiro L
(1)
Takai Y
(1)
Takebe K
(1)
Troyanovsky RB
(1)
Troyanovsky SM
(1)
Vendome J
(1)
Yamamoto Y
(1)
Yoshida A
(1)
Zheng C
(1)
 
Homo / hetero assembly  (2)
homo
(5)
hetero
(3)
 
Assembly composition  (2)
protein structure
(5)
protein/protein complex
(3)
 
Assembly polymer count  (2)
dimer
(7)
monomer
(1)
 
Resolution distribution
2.0 - 2.5
(2)
2.5 - 3
(1)
3.0 - 3.5
(3)
3.5 - 4
(1)
 
Release year distribution
2010 - 2015
(7)
2015 - 2020
(1)
 
Journal  (6)
Nat Commun
(2)
To be published
(2)
J Biol Chem
(1)
J Virol
(1)
Nat Struct Mol Biol
(1)
PLoS Pathog
(1)
 
Macromolecules
Organism superkingdom  (1)
Eukaryota
(8)
 
Organism name  (2)
Homo sapiens
(6)
Mus musculus
(2)
 
Molecule name  (8)
Herpes virus entry mediator C
(8)
Herpesvirus entry mediator C
(8)
HveC
(8)
Nectin cell adhesion molecule 1
(8)
Nectin-1
(8)
Poliovirus receptor-related protein 1
(8)
HIgR
(6)
Herpesvirus Ig-like receptor
(6)
 
Molecule type  (1)
Protein
(8)
 
Gene names  (8)
HVEC
(6)
NECTIN1
(6)
PRR1
(6)
PVRL1
(6)
Hvec
(2)
Nectin1
(2)
Prr1
(2)
Pvrl1
(2)
 
Interacting Molecules  (1)
Envelope glycoprotein D
(3)
 
Interacting ligands  (6)
NAG : 2-acetamido-2-deoxy-beta-D-glucopyranose
(2)
BMA : beta-D-mannopyranose
(1)
CIT : CITRIC ACID
(1)
FMT : FORMIC ACID
(1)
HEZ : HEXANE-1,6-DIOL
(1)
PG6 : 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
(1)
 
Sequence and Structure classification
CATH class  (1)
Mainly Beta
(8)
 
CATH topology  (1)
Immunoglobulin-like
(8)
 
Pfam accession / name  (3)
PF07686 : V-set
(7)
PF13927 : Ig_3
(7)
PF08205 : C2-set_2
(6)
 
Experimental Information
Diffraction protocol  (1)
Single wavelength
(7)
 
Diffraction radiation source type  (1)
Synchrotron
(7)
 
Diffraction source  (4)
SSRF BEAMLINE BL17U
(3)
SPRING-8 BEAMLINE BL44XU
(2)
APS BEAMLINE 14-BM-C
(1)
APS BEAMLINE 24-ID-E
(1)
 
Synchrotron site  (3)
SSRF
(3)
APS
(2)
SPring-8
(2)
 
Diffraction detector type  (1)
CCD
(7)
 
Refinement software  (2)
PHENIX
(5)
REFMAC
(3)
 
NMR
NMR software packages  (7)
ARIA
(1)
CYANA
(1)
NMRDraw
(1)
NMRPipe
(1)
Pronto
(1)
TALOS
(1)
VNMR
(1)
 
NMR Field Strength
700.0 - 800
(1)
 
Representative Structures
Representative Structures
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Entries 1 to 8 of 8
Entries 1 to 8 of 8
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Dimer structure of murine Nectin-1 D1
Sangawa T, Takebe K, Suzuki M
To be published
Source organism: Mus musculus  
Assembly composition: protein only structure
Assembly name: Nectin-1 (Preferred)   search this complex
PDBe complex ID: PDB-CPX-191630 (Preferred)   search this ID
PDBe-KB: Q9JKF6   
X-ray diffraction
2.24Å resolution
Released: 28 Dec 2016
Model geometry
Fit model/data
5b21
5b21
5b21
Crystal structure of human nectin-1 full ectodomain (D1-D3)
Harrison OJ, Brasch J, Shapiro L
Nat Struct Mol Biol (2012) [PMID: 22902367  ]
Source organism: Homo sapiens  
Assembly composition: protein only structure
Bound ligands: FMT    FMT   
Carbohydrate polymer components:
Molecule 1 - NAG(2)
Assembly name: Nectin-1 (Preferred)   search this complex
PDBe complex ID: PDB-CPX-172234 (Preferred)   search this ID
PDBe-KB: Q15223   
X-ray diffraction
3.2Å resolution
Released: 22 Aug 2012
Model geometry
Fit model/data
4fmf
4fmf
4fmf
Structure of HSV-2 gD bound to nectin-1
Lu G, Zhang N, Qi J, Li Y, Chen Z, Zheng C, Yan J, Gao GF
J Virol (2014) [PMID: 25231300  ]
Assembly composition: protein/protein complex
Bound ligands: NAG    NAG   
Carbohydrate polymer components:
Molecule 1 - NAG(2)
Assembly name: Nectin-1 and Envelope glycoprotein D (Preferred)   search this complex
PDBe complex ID: PDB-CPX-136626 (Preferred)   search this ID
PDBe-KB: Q15223    P03172   
X-ray diffraction
3.189Å resolution
Released: 1 Oct 2014
Model geometry
Fit model/data
4myw
4myw
4myw
Herpes simplex virus glycoprotein D bound to the human receptor nectin-1
Di Giovine P, Settembre EC, Bhargava AK, Luftig MA, Lou H, Cohen GH, Eisenberg RJ, Krummenacher C, Carfi A
PLoS Pathog (2011) [PMID: 21980294  ]
Assembly composition: protein/protein complex
Bound ligands: NAG    NAG   
Carbohydrate polymer components:
Molecule 1 - BMA(1), NAG(2)
Molecule 2 - NAG(2)
Assembly name: Nectin-1 and Envelope glycoprotein D (Preferred)   search this complex
PDBe complex ID: PDB-CPX-172233 (Preferred)   search this ID
PDBe-KB: Q15223    Q991M3   
X-ray diffraction
4Å resolution
Released: 12 Oct 2011
Model geometry
Fit model/data
3sku
3sku
3sku
Cell adhesion protein
Narita H, Nakagawa A, Suzuki M
J Biol Chem (2011) [PMID: 21325282  ]
Source organism: Homo sapiens  
Assembly composition: protein only structure
Bound ligands: CIT    HEZ   
Assembly name: Nectin-1 (Preferred)   search this complex
PDBe complex ID: PDB-CPX-172234 (Preferred)   search this ID
PDBe-KB: Q15223   
X-ray diffraction
2.804Å resolution
Released: 16 Feb 2011
Model geometry
Fit model/data
3alp
3alp
3alp
Crystal structure of nectin-1
Zhang N, Yan J, Lu G, Guo Z, Fan Z, Wang J, Shi Y, Qi J, Gao GF
Nat Commun (2011) [PMID: 22146396  ]
Source organism: Homo sapiens  
Assembly composition: protein only structure
Bound ligands: PG6    PG6   
Assembly name: Nectin-1 (Preferred)   search this complex
PDBe complex ID: PDB-CPX-172234 (Preferred)   search this ID
PDBe-KB: Q15223   
X-ray diffraction
2.499Å resolution
Released: 21 Mar 2012
Model geometry
Fit model/data
3u83
3u83
3u83
Binding of herpes simplex virus glycoprotein D to nectin-1 exploits host cell adhesion
Zhang N, Yan J, Lu G, Guo Z, Fan Z, Wang J, Shi Y, Qi J, Gao GF
Nat Commun (2011) [PMID: 22146396  ]
Assembly composition: protein/protein complex
Assembly name: Nectin-1 and Envelope glycoprotein D (Preferred)   search this complex
PDBe complex ID: PDB-CPX-172232 (Preferred)   search this ID
PDBe-KB: Q15223    Q69091   
X-ray diffraction
3.164Å resolution
Released: 21 Mar 2012
Model geometry
Fit model/data
3u82
3u82
3u82
Solution structure of the third Immunoglobulin-like domain of nectin-1
Clausen O, Poulsen FM
To be published
Source organism: Mus musculus  
Assembly composition: protein only structure
Assembly name: Nectin-1 (Preferred)   search this complex
PDBe complex ID: PDB-CPX-191629 (Preferred)   search this ID
PDBe-KB: Q9JKF6   
Solution NMR
Released: 14 Dec 2011
Model geometry
Fit model/data
Data not analysed
2l7j
2l7j
2l7j
Entries 1 to 8 of 8
Entries 1 to 8 of 8