Structure of PDB 4ros Chain A Binding Site BS02

Receptor Information
>4ros Chain A (length=318) Species: 419610 (Methylorubrum extorquens PA1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ARSKIALIGAGQIGGTLAHLAGLKELGDVVLFDIVDGVPQGKALDIAESA
PVDGFDAKYSGASDYSAIAGADVVIVTAGVPRKPGMSRDDLIGINLKVME
AVGAGIKEHAPDAFVICITNPLDAMVWALQKFSGLPTNKVVGMAGVLDSA
RFRHFLAEEFGVSVEDVTAFVLGGHGDDMVPLTRYSTVAGVPLTDLVKLG
WTTQEKLDAMVERTRKGGGEIVNLLKTGSAFYAPAASAIAMAESYLRDKK
RVLPCAAYLDGQYGIDGLYVGVPVVIGENGVERVLEVTFNDDEKAMFEKS
VNSVKGLIEACKSVNDKL
Ligand information
Ligand IDAPR
InChIInChI=1S/C15H23N5O14P2/c16-12-7-13(18-3-17-12)20(4-19-7)14-10(23)8(21)5(32-14)1-30-35(26,27)34-36(28,29)31-2-6-9(22)11(24)15(25)33-6/h3-6,8-11,14-15,21-25H,1-2H2,(H,26,27)(H,28,29)(H2,16,17,18)/t5-,6-,8-,9-,10-,11-,14-,15-/m1/s1
InChIKeySRNWOUGRCWSEMX-KEOHHSTQSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(OCC3OC(n1c2ncnc(N)c2nc1)C(O)C3O)OP(=O)(O)OCC4OC(O)C(O)C4O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)O)O)O)O)O)N
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)O)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH](O)[CH](O)[CH]4O)[CH](O)[CH]3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@@H](O)[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O
FormulaC15 H23 N5 O14 P2
NameADENOSINE-5-DIPHOSPHORIBOSE
ChEMBLCHEMBL1231026
DrugBank
ZINCZINC000017654550
PDB chain4ros Chain A Residue 404 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4ros Crystal structure of Methylobacterium extorquens malate dehydrogenase complexed with oxaloacetate and adenosine-5-diphosphoribose
Resolution1.95 Å
Binding residue
(original residue number in PDB)		G12 Q13 I14 D34 I35 T78 A79 G80 V81 P82 V99 T120 N121
Binding residue
(residue number reindexed from 1)		G11 Q12 I13 D33 I34 T77 A78 G79 V80 P81 V98 T119 N120
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) R89 D149 R152 H176
Catalytic site (residue number reindexed from 1) R88 D148 R151 H175
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4ros, PDBe:4ros, PDBj:4ros
PDBsum4ros
PubMed
UniProtA9W386|MDH_METEP Malate dehydrogenase (Gene Name=mdh)

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