Structure of PDB 3gvi Chain B Binding Site BS01

Receptor Information

>3gvi Chain B (length=314) Species: 359391 (Brucella abortus 2308)

ARNKIALIGSGMIGGTLAHLAGLKELGDVVLFDIAEGTPQGKGLDIAESS
PVDGFDAKFTGANDYAAIEGADVVIVTAGVPRKDDLLGINLKVMEQVGAG
IKKYAPEAFVICITNPLDAMVWALQKFSGLPAHKVVGMAGVLDSARFRYF
LSEEFNVSVEDVTVFVLGGHGDSMVPLARYSTVAGIPLPDLVKMGWTSQD
KLDKIIQRTRDGGAEIVGLLKTGSAFYAPAASAIQMAESYLKDKKRVLPV
AAQLSGQYGVKDMYVGVPTVIGANGVERIIEIDLDKDEKAQFDKSVASVA
GLCEACIGIAPSLK

Ligand information

• Ligand ID: ADP
• InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
• InChIKey: XTWYTFMLZFPYCI-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
• Formula: C10 H15 N5 O10 P2
• Name: ADENOSINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL14830
• DrugBank: DB16833
• ZINC: ZINC000012360703
• PDB chain: 3gvi Chain B Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3gvi Crystal structure of Lactate/malate dehydrogenase from Brucella melitensis in complex with ADP
• Resolution: 2.25 Å
• Binding residue (original residue number in PDB): G12 M13 I14 D34 I35 A79 G80
• Binding residue (residue number reindexed from 1): G11 M12 I13 D33 I34 A78 G79
• Annotation score: 3

Enzymatic activity

• Catalytic site (original residue number in PDB): D149 R152 H176
• Catalytic site (residue number reindexed from 1): D143 R146 H170
• Enzyme Commision number: 1.1.1.37: malate dehydrogenase.

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0004459 L-lactate dehydrogenase activity
• GO:0016491 oxidoreductase activity
• GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
• GO:0030060 L-malate dehydrogenase (NAD+) activity

Biological Process

• GO:0006089 lactate metabolic process
• GO:0006090 pyruvate metabolic process
• GO:0006099 tricarboxylic acid cycle
• GO:0019752 carboxylic acid metabolic process

External links

• PDB: RCSB:3gvi, PDBe:3gvi, PDBj:3gvi
• PDBsum: 3gvi
• UniProt: Q2YLR9|MDH_BRUA2 Malate dehydrogenase (Gene Name=mdh)