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Structure of PDB 6s83 Chain B Binding Site BS04

Receptor Information

>6s83 Chain B (length=400) Species: 186497 (Pyrococcus furiosus DSM 3638)

ARNIVVEEIVRTPVEMQQVELVERKGIGHPDSIADGIAEAVSRALCREYI
RRYGVILHHNTDQVEVVGGRAYPRFGGGEVVKPIYILLSGRAVELVDQEL
FPVHEVAIKAAKNYLKNAIRHLDVENHVIIDSRIGQGSVDLVSVFNKARE
NPIPLANDTSFGVGYAPLSETERLVLETEKLLNSEKFKKEYPAVGEDIKV
MGLRRGNEIDLTIAAAIVDSEVATPKEYLEVKDKIKEAVEELAKEITSRK
VNIYVNTADDPERGIYYITVTGTSAEAGDDGSVGRGNRVNGLITPNRHMS
MEAAAGKNPVSHVGKIYNILAMLIAEDIAKTLPVEEVYVRILSQIGKPID
QPLVASIQVIPKPGHSVKEFEKDAYSIADEWLANITKVQKMILEDKISVF

Ligand information

• Ligand ID: ACP
• InChI: InChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-31(24,25)28-30(22,23)4-29(19,20)21/h2-3,5,7-8,11,17-18H,1,4H2,(H,22,23)(H,24,25)(H2,12,13,14)(H2,19,20,21)/t5-,7-,8-,11-/m1/s1
• InChIKey: UFZTZBNSLXELAL-IOSLPCCCSA-N
• SMILES:
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)C[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)CP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(CP(=O)(O)O)O)O)O)N
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(CP(=O)(O)O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@](O)(=O)C[P](O)(O)=O)[C@@H](O)[C@H]3O
• Formula: C11 H18 N5 O12 P3
• Name: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER;
  ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE
• ChEMBL: CHEMBL133463
• DrugBank: DB03909
• ZINC: ZINC000008295124
• PDB chain: 6s83 Chain B Residue 504

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6s83 Structures of catalytic cycle intermediates of the Pyrococcus furiosus methionine adenosyltransferase demonstrate negative cooperativity in the archaeal orthologues.
• Resolution: 2.336 Å
• Binding residue (original residue number in PDB): K26 H30 D198 K200 A215 Y268 S275
• Binding residue (residue number reindexed from 1): K25 H29 D197 K199 A214 Y267 S274
• Annotation score: 3

Enzymatic activity

• Enzyme Commision number: 2.5.1.6: methionine adenosyltransferase.

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0004478 methionine adenosyltransferase activity
• GO:0005524 ATP binding
• GO:0016740 transferase activity

Biological Process

• GO:0006556 S-adenosylmethionine biosynthetic process
• GO:0006730 one-carbon metabolic process

External links

• PDB: RCSB:6s83, PDBe:6s83, PDBj:6s83
• PDBsum: 6s83
• PubMed: 31962159
• UniProt: Q8TZW1|METK_PYRFU S-adenosylmethionine synthase (Gene Name=mat)

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