Structure of PDB 6t9w Chain B Binding Site BS01

Receptor Information

>6t9w Chain B (length=383) Species: 682795 (Granulicella mallensis MP5ACTX8)

AKILCVLYDDPITGYPKSYARADVPKIDHYPGGQTAPTPKQIDFTPGELL
GSVSGELGLRKYLEGLGHTLVVTSDKEGEDSVFERELPDAEIVISQPFWP
AYLTPERIAKAKKLKLAVTAGIGSDHVDLEAAIKNGITVAEVTYSNSISV
SEHVVMMILSLVRNYIPSYQWVIKGGWNIADCVERSYDLEAMHVGTVAAG
RIGLAVLKRLKPFDVKLHYFARHRLPESVENELGLTYHPSVEDMVKVCDV
VTINAPLHPGTLDLFNDELISKMKRGAYLVNTARGKICNRDAVVRALESG
QLAGYAGDVWFPQPAPKDHPWRTMPHHGMTPHISGTSLSAQARYAAGTRE
ILECWFEERPIREEYLIVDGGKLAGTGAHSYTV

Ligand information

• Ligand ID: NAP
• InChI: InChI=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
• InChIKey: XJLXINKUBYWONI-NNYOXOHSSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1cc(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 3.341: NC(=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 3.341: NC(=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 1.5.0: c1cc(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
• Formula: C21 H28 N7 O17 P3
• Name: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE;
  2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
• ChEMBL: CHEMBL295069
• DrugBank: DB03461
• PDB chain: 6t9w Chain B Residue 801

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6t9w From the Amelioration of a NADP+-dependent Formate Dehydrogenase to the Discovery of a New Enzyme: Round Trip from Theory to Practice
• Resolution: 2.15 Å
• Binding residue (original residue number in PDB): I123 N147 S148 V151 A199 G201 R202 I203 F221 R223 P257 H259 T262 T283 A284 R285 D309 H333 S335 G336 S381
• Binding residue (residue number reindexed from 1): I122 N146 S147 V150 A198 G200 R201 I202 F220 R222 P256 H258 T261 T282 A283 R284 D308 H332 S334 G335 S380
• Annotation score: 3

Enzymatic activity

• Enzyme Commision number: 1.17.1.9: formate dehydrogenase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0008863 formate dehydrogenase (NAD+) activity
• GO:0016491 oxidoreductase activity
• GO:0016614 oxidoreductase activity, acting on CH-OH group of donors
• GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
• GO:0051287 NAD binding

Biological Process

• GO:0042183 formate catabolic process

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:6t9w, PDBe:6t9w, PDBj:6t9w
• PDBsum: 6t9w
• UniProt: G8NTI5