Ligands and environments ‹ 2oxt ‹ Protein Data Bank in Europe (PDBe)

1 bound ligand:

SAM 300(A) Environment details ›

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

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setting document base to "https://www.ebi.ac.uk/pdbe/entry/pdb/2oxt/ligands"

Jmol Version: 14.3.6_2014.08.17b 2014-08-17 17:24

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Jmol applet _PDBE_JMOL__6131911740244833__ ready

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

script 1 started

FileManager.getAtomSetCollectionFromFile(https://www.ebi.ac.uk/pdbe/entry-files/download/2oxt.cif)

FileManager opening 1 https://www.ebi.ac.uk/pdbe/entry-files/download/2oxt.cif

The Resolver thinks MMCif

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

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

-- required by J.adapter.readers.cif.MMCifReader

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

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

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

-- required by J.renderbio.BioShapeRenderer

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

TITLE: Structural bases for substrate recognition and activity in Meaban virus nucleoside-2'-O-methyltransferase

Setting space group name to HM:P 43

found biomolecule 1: A,E

found biomolecule 2: B,F,I

found biomolecule 3: C,G,J

found biomolecule 4: D,H,K

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/javajs/api/EigenInterface.js

-- required by JU.Eigen

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

Time for openFile(*2oxt): 1330 ms

reading 8409 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

8409 atoms created

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

TITLE: Structural bases for substrate recognition and activity in Meaban virus nucleoside-2'-O-methyltransferase

found biomolecule 1: A,E

found biomolecule 2: B,F,I

found biomolecule 3: C,G,J

found biomolecule 4: D,H,K

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

Script completed

Jmol script terminated

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-- required by JV.PropertyManager

script 2 started

antialiasDisplay = true

antialiasTranslucent = true

debugScript = false

showScript = 0

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

-- required by J.shapesurface.Contact

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

-- required by J.shapesurface.Isosurface

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

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

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: 44

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

Contacts: 8 with net volume 4.476100250784482 A^3

RasMol pseudo-hbond calculation

0 hydrogen bonds

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

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-- required by JV.OutputManagerJS

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-- required by javajs.img.Huffman

s://www.ebi.ac.uk/pdbe/software/jmol-future/jsmol/j2s/javajs/api/GenericImageEncoder.js

-- required by javajs.img.ImageEncoder

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: 45

Contacts: 8 with net volume 5.130494847656072 A^3

RasMol pseudo-hbond calculation

3 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: 41

Contacts: 9 with net volume 11.899121374421252 A^3

RasMol pseudo-hbond calculation

2 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: 39

Contacts: 7 with net volume 5.848558807845601 A^3

RasMol pseudo-hbond calculation

2 hydrogen bonds

Script completed

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SAM 300(B) Environment details ›

SAM 300(C) Environment details ›

SAM 300(D) Environment details ›

No modified residues

PDBe › 2oxt › Ligands and Environments

1 bound ligand:

Quick links

2oxt › Ligands and Environments