Ligands and environments ‹ 6t3m ‹ Protein Data Bank in Europe (PDBe)

4 bound ligands:

NAG 301(H) Environment details ›

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s://www.ebi.ac.uk/pdbe/software/jmol-future/jsmol/j2s/core/corescript.z.js

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FileManager.getAtomSetCollectionFromFile(https://www.ebi.ac.uk/pdbe/entry-files/download/6t3m.cif)

FileManager opening 1 https://www.ebi.ac.uk/pdbe/entry-files/download/6t3m.cif

The Resolver thinks MMCif

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s://www.ebi.ac.uk/pdbe/software/jmol-future/jsmol/j2s/JU/CifDataParser.js

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s://www.ebi.ac.uk/pdbe/software/jmol-future/jsmol/j2s/J/shape/Mesh.js

TITLE: Thrombin in Complex with a D-Phe-Pro-p-phenol derivative

Setting space group name to Hall:C 2y

Setting space group name to HM:C 1 2 1

found biomolecule 1: A,B,C,D,E,F,G,H,I,J,K,L

s://www.ebi.ac.uk/pdbe/software/jmol-future/jsmol/j2s/core/coresym.z.js

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

Setting space group name to HM:C 1 2 1

Setting space group name to Hall:C 2y

s://www.ebi.ac.uk/pdbe/software/jmol-future/jsmol/j2s/JU/Tensor.js

s://www.ebi.ac.uk/pdbe/software/jmol-future/jsmol/j2s/JU/Eigen.js

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-- required by JU.Eigen

s://www.ebi.ac.uk/pdbe/software/jmol-future/jsmol/j2s/JU/EigenSort.js

Time for openFile(*6t3m): 2981 ms

reading 5032 atoms

ModelSet: haveSymmetry:false haveUnitcells:true haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

model 1.1 alternative locations: AB

Default Van der Waals type for model set to Babel

5032 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

TITLE: Thrombin in Complex with a D-Phe-Pro-p-phenol derivative

found biomolecule 1: A,B,C,D,E,F,G,H,I,J,K,L

Script completed

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script 2 started

antialiasDisplay = true

antialiasTranslucent = true

debugScript = false

showScript = 0

chainCaseSensitive = true

measurementUnits = "angstroms"

autobond = true

forceAutoBond = true

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-- required by J.shapesurface.Contact

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-- required by J.shapesurface.Isosurface

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s://www.ebi.ac.uk/pdbe/software/jmol-future/jsmol/j2s/JU/ContactPair.js

contact ID "hb" {environmentAtoms} hbond color TRANSLUCENT 0.2 purple;

Contact pairs: 7

Contacts: 0

Standard Hbond calculation

2 hydrogen bonds

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script 3 started

antialiasDisplay = true

antialiasTranslucent = true

debugScript = false

showScript = 0

chainCaseSensitive = true

measurementUnits = "angstroms"

autobond = true

forceAutoBond = true

contact ID "hb" {environmentAtoms} hbond color TRANSLUCENT 0.2 purple;

Contact pairs: 6

Contacts: 0

Standard Hbond calculation

0 hydrogen bonds

Script completed

Jmol script terminated

script 4 started

antialiasDisplay = true

antialiasTranslucent = true

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showScript = 0

chainCaseSensitive = true

measurementUnits = "angstroms"

autobond = true

forceAutoBond = true

contact ID "hb" {environmentAtoms} hbond color TRANSLUCENT 0.2 purple;

Contact pairs: 8

s://www.ebi.ac.uk/pdbe/software/jmol-future/jsmol/j2s/J/jvxl/readers/IsoIntersectReader.js

Contacts: 8 with net volume 3.101124444896242 A^3

Standard Hbond calculation

6 hydrogen bonds

Script completed

Jmol script terminated

script 5 started

antialiasDisplay = true

antialiasTranslucent = true

debugScript = false

showScript = 0

chainCaseSensitive = true

measurementUnits = "angstroms"

autobond = true

forceAutoBond = true

contact ID "hb" {environmentAtoms} hbond color TRANSLUCENT 0.2 purple;

Contact pairs: 8

Contacts: 4 with net volume 0.6992379082587212 A^3

Standard Hbond calculation

2 hydrogen bonds

Script completed

Jmol script terminated

script 6 started

antialiasDisplay = true

antialiasTranslucent = true

debugScript = false

showScript = 0

chainCaseSensitive = true

measurementUnits = "angstroms"

autobond = true

forceAutoBond = true

contact ID "hb" {environmentAtoms} hbond color TRANSLUCENT 0.2 purple;

Contact pairs: 12

Contacts: 10 with net volume 1.3041895357152566 A^3

Standard Hbond calculation

4 hydrogen bonds

Script completed

Jmol script terminated

script 7 started

antialiasDisplay = true

antialiasTranslucent = true

debugScript = false

showScript = 0

chainCaseSensitive = true

measurementUnits = "angstroms"

autobond = true

forceAutoBond = true

contact ID "hb" {environmentAtoms} hbond color TRANSLUCENT 0.2 purple;

Contact pairs: 1

Contacts: 1 with net volume 0.02556317498379041 A^3

Standard Hbond calculation

0 hydrogen bonds

Script completed

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MD8 302(H) Environment details ›

MD8 303(H) Environment details ›

PO4 304(H) Environment details ›

NA 305(H) Environment details ›

NA 306(H) Environment details ›

Protein Data Bank in Europe

4 bound ligands:

1 modified residue:

Quick links

PDBe › 6t3m › Ligands and Environments

4 bound ligands:

1 modified residue:

Quick links

6t3m › Ligands and Environments