Ligands and environments ‹ 4a3f ‹ Protein Data Bank in Europe (PDBe)

3 bound ligands:

APC 2455(A) Environment details ›

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FileManager.getAtomSetCollectionFromFile(https://www.ebi.ac.uk/pdbe/entry-files/download/4a3f.cif)

FileManager opening 1 https://www.ebi.ac.uk/pdbe/entry-files/download/4a3f.cif

The Resolver thinks MMCif

s://www.ebi.ac.uk/pdbe/software/jmol-future/jsmol/j2s/J/adapter/readers/cif/MMCifReader.js

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TITLE: Structural basis of initial RNA polymerase II transcription.

Setting space group name to HM:C 2 2 21

found biomolecule 1: A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y

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

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

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

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

Time for openFile(*4a3f): 5015 ms

reading 32010 atoms

ModelSet: haveSymmetry:false haveUnitcells:true 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

32010 atoms created

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

TITLE: Structural basis of initial RNA polymerase II transcription.

found biomolecule 1: A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y

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script 2 started

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chainCaseSensitive = true

measurementUnits = "angstroms"

autobond = true

forceAutoBond = true

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

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-- required by J.shapesurface.Isosurface

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

Contact pairs: 2

Contacts: 0

RasMol pseudo-hbond calculation

0 hydrogen bonds

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

Script completed

Jmol script terminated

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script 3 started

antialiasDisplay = true

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showScript = 0

chainCaseSensitive = true

measurementUnits = "angstroms"

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

Contact pairs: 0

Contacts: 0

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: 0

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: 0

Contacts: 0

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

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

Contact pairs: 0

Contacts: 0

RasMol pseudo-hbond calculation

0 hydrogen bonds

Script completed

Jmol script terminated

script 7 started

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chainCaseSensitive = true

measurementUnits = "angstroms"

autobond = true

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

Contact pairs: 0

Contacts: 0

RasMol pseudo-hbond calculation

0 hydrogen bonds

Script completed

Jmol script terminated

script 8 started

antialiasDisplay = true

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debugScript = false

showScript = 0

chainCaseSensitive = true

measurementUnits = "angstroms"

autobond = true

forceAutoBond = true

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

Contact pairs: 0

Contacts: 0

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: 0

Contacts: 0

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

forceAutoBond = true

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

Contact pairs: 0

Contacts: 0

RasMol pseudo-hbond calculation

0 hydrogen bonds

Script completed

Jmol script terminated

script 11 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: 24

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

Contacts: 13 with net volume 8.424049868773244 A^3

RasMol pseudo-hbond calculation

2 hydrogen bonds

Script completed

Jmol script terminated

script 12 started

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ZN 2456(A) Environment details ›

ZN 2457(A) Environment details ›

ZN 2225(B) Environment details ›

ZN 1269(C) Environment details ›

ZN 1121(I) Environment details ›

ZN 1122(I) Environment details ›

ZN 1066(J) Environment details ›

ZN 1071(L) Environment details ›

MG 2458(A) Environment details ›

Protein Data Bank in Europe

3 bound ligands:

1 modified residue:

Quick links

PDBe › 4a3f › Ligands and Environments

3 bound ligands:

1 modified residue:

Quick links

4a3f › Ligands and Environments