Structure of PDB 3nkv Chain B Binding Site BS03

Receptor Information

>3nkv Chain B (length=169) Species: 9606 (Homo sapiens)

EYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELD
GKTIKLQIWDTAGQERFRTITSSYYRGAHGIIVVYDVTDQESYANVKQWL
QEIDRYASNVNKLLVGNKSDLTTKKVVDNTTAKEFADSLGIPFLETSAKN
ATNVEQAFMTMAAEIKKRM

Ligand information

• Ligand ID: AMP
• InChI: InChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
• InChIKey: UDMBCSSLTHHNCD-KQYNXXCUSA-N
• SMILES:
  CACTVS 3.370: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
  CACTVS 3.370: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.7.6: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N
  ACDLabs 12.01: O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  OpenEye OEToolkits 1.7.6: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
• Formula: C10 H14 N5 O7 P
• Name: ADENOSINE MONOPHOSPHATE
• ChEMBL: CHEMBL752
• DrugBank: DB00131
• ZINC: ZINC000003860156
• PDB chain: 3nkv Chain B Residue 600

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3nkv The Legionella effector protein DrrA AMPylates the membrane traffic regulator Rab1b.
• Resolution: 1.7 Å
• Binding residue (original residue number in PDB): F45 W62 Y77
• Binding residue (residue number reindexed from 1): F42 W59 Y74
• Annotation score: 2

Enzymatic activity

• Catalytic site (original residue number in PDB): Q67
• Catalytic site (residue number reindexed from 1): Q64
• Enzyme Commision number: 3.6.5.2: small monomeric GTPase.

Gene Ontology

Molecular Function

• GO:0003924 GTPase activity
• GO:0005525 GTP binding

External links

• PDB: RCSB:3nkv, PDBe:3nkv, PDBj:3nkv
• PDBsum: 3nkv
• PubMed: 20651120
• UniProt: Q9H0U4|RAB1B_HUMAN Ras-related protein Rab-1B (Gene Name=RAB1B)