Structure of PDB 1bdm Chain B Binding Site BS01

Receptor Information
>1bdm Chain B (length=327) Species: 274 (Thermus thermophilus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKAPVRVAVTGAAGQIGYSLLFRIAAGEMLGKDQPVILQLLEIPQAMKAL
EGVVMELEDCAFPLLAGLEATDDPDVAFKDADYALLVGAAPRKAGMERRD
LLQVNGKIFTEQGRALAEVAKKDVKVLVVGNPANTNALIAYKNAPGLNPR
NFTAMTRLDHNRAKAQLAKKTGTGVDRIRRMTVWGNHSSIMFPDLFHAEV
DGRPALELVDMEWYEKVFIPTVAQRGAAIIQARGASSAASAANAAIEHIR
DWALGTPEGDWVSMAVPSQGEYGIPEGIVYSFPVTAKDGAYRVVEGLEIN
EFARKRMEITAQELLDEMEQVKALGLI
Ligand information
Ligand IDNAX
InChIInChI=1S/C21H31N7O15P2/c22-17-12-19(25-6-24-17)28(7-26-12)21-16(33)14(31)10(42-21)5-40-45(37,38)43-44(35,36)39-4-9-13(30)15(32)20(41-9)27-3-8(18(23)34)1-2-11(27)29/h3,6-7,9-11,13-16,20-21,29-33H,1-2,4-5H2,(H2,23,34)(H,35,36)(H,37,38)(H2,22,24,25)/t9-,10-,11+,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyIDBZKGQRLBFUFQ-VPHRTNKSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC(=O)C1=CN([CH](O)CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
CACTVS 3.341NC(=O)C1=CN([C@@H](O)CC1)[C@@H]2O[C@H](CO[P@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=C(CCC5O)C(=O)N)O)O)O)O)N
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)N5C=C(CC[C@@H]5O)C(=O)N)O)O)O)O)N
FormulaC21 H31 N7 O15 P2
NameBETA-6-HYDROXY-1,4,5,6-TETRHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
ChEMBL
DrugBank
ZINCZINC000008219662
PDB chain1bdm Chain B Residue 334 [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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PDB1bdm Determinants of protein thermostability observed in the 1.9-A crystal structure of malate dehydrogenase from the thermophilic bacterium Thermus flavus.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		G10 G13 Q14 I15 E41 I42 V86 G87 I107 V128 G129 N130 M154 H186
Binding residue
(residue number reindexed from 1)		G11 G14 Q15 I16 E42 I43 V87 G88 I108 V129 G130 N131 M155 H187
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) D158 H186
Catalytic site (residue number reindexed from 1) D159 H187
Enzyme Commision number 1.1.1.37: malate dehydrogenase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0016491 oxidoreductase activity
GO:0016615 malate dehydrogenase 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:0006099 tricarboxylic acid cycle
GO:0006107 oxaloacetate metabolic process
GO:0006108 malate metabolic process
GO:0006734 NADH metabolic process
GO:0019752 carboxylic acid metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1bdm, PDBe:1bdm, PDBj:1bdm
PDBsum1bdm
PubMed8471603
UniProtP10584|MDH_THETH Malate dehydrogenase (Gene Name=mdh)

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