Structure of PDB 5vj7 Chain A Binding Site BS03

Receptor Information

>5vj7 Chain A (length=462) Species: 1185654 (Pyrococcus furiosus COM1)

IKERVPTPERSVGERVRDFGEVNLGYSWELALREAERCLQCPVEYAPCIK
GCPVHINIPGFIKALRENRDNPSKAVREALRIIWRDNTLPAITGRVCPQE
EQCEGACVVGKVGDPINIGKLERFVADYAREHGIDDELLLEEIKGIKRNG
KKVAIIGAGPAGLTCAADLAKMGYEVTIYEALHQPGGVLTYGIPEFRLPK
EILRKELKKLSLLGVEIKTDHIVGKTITIQELLQEYDAVFIGTGAGTPKL
PNIPGINLNGIYSANEFLTRINLMKAYKFPEYDTPIVVGKKVVVIGAGNT
AMDAARSALRLGAEVTIAYRRGREDMTARIEEVKHAEEEGVKFMFFVNPV
EFIGDENGNVKAVKFEKMKPGKRKIVGTGEYITVEADTVIIAIGQTPNKV
LWRATPELKVDEWGRIVVDENLMTSIPGVFAGGDAIRGEATVILAMGDGR
KAAKAIHQYLSK

Ligand information

• Ligand ID: FAD
• InChI: InChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
• InChIKey: VWWQXMAJTJZDQX-UYBVJOGSSA-N
• SMILES:
  CACTVS 3.341: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
  OpenEye OEToolkits 1.5.0: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
  OpenEye OEToolkits 1.5.0: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
  CACTVS 3.341: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
  ACDLabs 10.04: O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
• Formula: C27 H33 N9 O15 P2
• Name: FLAVIN-ADENINE DINUCLEOTIDE
• ChEMBL: CHEMBL1232653
• DrugBank: DB03147
• ZINC: ZINC000008215434
• PDB chain: 5vj7 Chain A Residue 503

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5vj7 Two functionally distinct NADP(+)-dependent ferredoxin oxidoreductases maintain the primary redox balance of Pyrococcus furiosus.
• Resolution: 2.55 Å
• Binding residue (original residue number in PDB): V100 G161 G163 P164 E184 A185 L186 G191 V192 I197 R201 V227 T247 G248 N303 T304 D445 T452 V453 A456
• Binding residue (residue number reindexed from 1): V96 G157 G159 P160 E180 A181 L182 G187 V188 I193 R197 V223 T243 G244 N299 T300 D434 T441 V442 A445
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): P164 I197 P198 F200 D307 I454 M457 G458
• Catalytic site (residue number reindexed from 1): P160 I193 P194 F196 D303 I443 M446 G447

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0016491 oxidoreductase activity
• GO:0046872 metal ion binding
• GO:0051536 iron-sulfur cluster binding
• GO:0051539 4 iron, 4 sulfur cluster binding

External links

• PDB: RCSB:5vj7, PDBe:5vj7, PDBj:5vj7
• PDBsum: 5vj7
• PubMed: 28705933
• UniProt: I6V148