Ligands and environments ‹ 8jj2 ‹ Protein Data Bank in Europe (PDBe)

1 bound ligand:

NAG 901(A) Environment details ›

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Jmol applet _PDBE_JMOL__994407349178809__ ready

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script 1 started

FileManager.getAtomSetCollectionFromFile(https://www.ebi.ac.uk/pdbe/entry-files/download/8jj2.cif)

FileManager opening 1 https://www.ebi.ac.uk/pdbe/entry-files/download/8jj2.cif

The Resolver thinks MMCif

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TITLE: Structural basis for antibody-mediated NMDA receptor clustering and endocytosis in autoimmune encephalitis.

Setting space group name to HM:P 1

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

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(*8jj2): 1637 ms

reading 26196 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

26196 atoms created

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

TITLE: Structural basis for antibody-mediated NMDA receptor clustering and endocytosis in autoimmune encephalitis.

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

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

Contact pairs: 3

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

Contacts: 2 with net volume 1.95827099867955 A^3

RasMol pseudo-hbond calculation

0 hydrogen bonds

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-- required by javajs.img.ImageEncoder

script 3 started

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autobond = true

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

Contact pairs: 10

Contacts: 3 with net volume 2.5292106455427046 A^3

RasMol pseudo-hbond calculation

0 hydrogen bonds

Script completed

Jmol script terminated

script 4 started

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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 1.401281772385989 A^3

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: 5

Contacts: 1 with net volume 0.9169210304273933 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: 3

Contacts: 0

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: 4

Contacts: 1 with net volume 0.06648071070446102 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: 2

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: 2

Contacts: 1 with net volume 1.7470725556977604 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

forceAutoBond = true

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

Contact pairs: 6

Contacts: 2 with net volume 0.9644019648281745 A^3

RasMol pseudo-hbond calculation

0 hydrogen bonds

Script completed

Jmol script terminated

script 11 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: 3

Contacts: 2 with net volume 0.7538836443785254 A^3

RasMol pseudo-hbond calculation

0 hydrogen bonds

Script completed

Jmol script terminated

script 12 started

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Jmol script terminated

script 13 started

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script 14 started

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NAG 901(B) Environment details ›

NAG 902(B) Environment details ›

NAG 903(B) Environment details ›

NAG 904(B) Environment details ›

NAG 901(D) Environment details ›

NAG 902(D) Environment details ›

NAG 903(D) Environment details ›

NAG 1(G) Environment details ›

NAG 2(G) Environment details ›

No modified residues

PDBe › 8jj2 › Ligands and Environments

1 bound ligand:

Quick links

8jj2 › Ligands and Environments