Ligands and environments ‹ 9bvk ‹ Protein Data Bank in Europe (PDBe)

3 bound ligands:

A1AVC 801(A) Environment details ›

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FileManager.getAtomSetCollectionFromFile(https://www.ebi.ac.uk/pdbe/entry-files/download/9bvk.cif)

FileManager opening 1 https://www.ebi.ac.uk/pdbe/entry-files/download/9bvk.cif

The Resolver thinks MMCif

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TITLE: Structural basis of vitamin K dependent gamma-carboxylation

Setting space group name to HM:P 1

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

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

Time for openFile(*9bvk): 1852 ms

reading 6213 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

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

Default Van der Waals type for model set to Jmol

6213 atoms created

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

TITLE: Structural basis of vitamin K dependent gamma-carboxylation

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

Script completed

Jmol script terminated

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forceAutoBond = true

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

Contact pairs: 2

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

Contacts: 1 with net volume 0.42899601917444635 A^3

RasMol pseudo-hbond calculation

0 hydrogen bonds

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script 3 started

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forceAutoBond = true

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

Contact pairs: 12

Contacts: 4 with net volume 3.9390690022450587 A^3

RasMol pseudo-hbond calculation

0 hydrogen bonds

Script completed

Jmol script terminated

script 4 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: 0

RasMol pseudo-hbond calculation

0 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: 11

Contacts: 4 with net volume 0.7913530882970795 A^3

RasMol pseudo-hbond calculation

0 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: 2

Contacts: 1 with net volume 1.7904967111635628 A^3

RasMol pseudo-hbond calculation

0 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: 8

Contacts: 1 with net volume 1.7904967111635628 A^3

RasMol pseudo-hbond calculation

0 hydrogen bonds

Script completed

Jmol script terminated

script 8 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: 4

Contacts: 1 with net volume 0.0018717266693471027 A^3

RasMol pseudo-hbond calculation

0 hydrogen bonds

Script completed

Jmol script terminated

script 9 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: 18

Contacts: 1 with net volume 2.0626265784922473 A^3

RasMol pseudo-hbond calculation

0 hydrogen bonds

Script completed

Jmol script terminated

script 10 started

antialiasDisplay = true

antialiasTranslucent = true

debugScript = false

showScript = 0

chainCaseSensitive = true

measurementUnits = "angstroms"

autobond = true

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

Contact pairs: 26

Contacts: 3 with net volume 0.1303117502176641 A^3

RasMol pseudo-hbond calculation

0 hydrogen bonds

Script completed

Jmol script terminated

script 11 started

antialiasDisplay = true

antialiasTranslucent = true

debugScript = false

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measurementUnits = "angstroms"

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

Contact pairs: 27

Contacts: 2 with net volume 1.0721492612472294 A^3

RasMol pseudo-hbond calculation

0 hydrogen bonds

Script completed

Jmol script terminated

script 12 started

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6PL 802(A) Environment details ›

6PL 803(A) Environment details ›

NAG 804(A) Environment details ›

NAG 1(B) Environment details ›

NAG 2(B) Environment details ›

NAG 1(C) Environment details ›

NAG 2(C) Environment details ›

NAG 1(D) Environment details ›

NAG 2(D) Environment details ›

No modified residues

PDBe › 9bvk › Ligands and Environments

3 bound ligands:

Quick links

9bvk › Ligands and Environments