Structure of PDB 8hho Chain A Binding Site BS01

Receptor Information
>8hho Chain A (length=416) Species: 49899 (Thermococcus profundus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IDPFEMAVKQLERAAQYMDISEEALEWLKKPMRIVEVSVPIEMDDGSVKV
FTGFRVQHNWARGPTKGGIRWHPAETLSTVKALATWMTWKVAVVDLPYGG
GKGGIIVNPKELSEREQERLARAYIRAVYDVIGPWTDIPAPDVYTNPKIM
GWMMDEYETIMRRKGPAFGVITGKPLSIGGSLGRGTATAQGAIFTIREAA
KALGIDLKGKKIAVQGYGNAGYYTAKLAKEQLGMTVVAVSDSRGGIYNPD
GLDPDEVLKWKREHGSVKDFPGATNITNEELLELEVDVLAPAAIEEVITE
KNADNIKAKIVAEVANGPVTPEADDILREKGILQIPDFLCNAGGVTVSYF
EWVQNINGYYWTEEEVREKLDKKMTKAFWEVYNTHKDKNIHMRDAAYVVA
VSRVYQAMKDRGWVKK
Ligand information
Ligand IDNAP
InChIInChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyXJLXINKUBYWONI-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
CACTVS 3.341NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
CACTVS 3.341NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@@](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
FormulaC21 H28 N7 O17 P3
NameNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE;
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
ChEMBLCHEMBL295069
DrugBankDB03461
ZINC
PDB chain8hho Chain A Residue 501 [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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PDB8hho Coenzyme-binding pathway on glutamate dehydrogenase suggested from multiple-binding sites visualized by cryo-electron microscopy.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		N149 P150 D244
Binding residue
(residue number reindexed from 1)		N146 P147 D241
Annotation score4
Enzymatic activity
Enzyme Commision number 1.4.1.3: glutamate dehydrogenase [NAD(P)(+)].
Gene Ontology
Molecular Function
GO:0004352 glutamate dehydrogenase (NAD+) activity
GO:0004353 glutamate dehydrogenase [NAD(P)+] activity
GO:0004354 glutamate dehydrogenase (NADP+) activity
GO:0016491 oxidoreductase activity
GO:0016639 oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor
Biological Process
GO:0006520 amino acid metabolic process
GO:0006538 glutamate catabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:8hho, PDBe:8hho, PDBj:8hho
PDBsum8hho
PubMed37682540
UniProtO74024|DHE3_THEPR Glutamate dehydrogenase (Gene Name=gdhA)

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