Structure of PDB 7npa Chain D Binding Site BS07

Receptor Information
>7npa Chain D (length=617) Species: 523845 (Methanothermococcus thermolithotrophicus DSM 2095) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YEWKLNDIVDNGICAKCGTCTVVCPNGILTFEDRPKLTEECLRKGNGMCF
EVCPRVSSGKYQIKIREKFKEEYYYGKGDVEGQDGGVVTTFLKYLLKNKK
IDGAIVVGDECWKPVSLIVQNEEDLMNTTKSKYTVSTLEALKTAGEMGLE
KVAVVGLPCQINGLRKLQYFQYLAKHDGELGKNGKPVKLPKIEYLIGLLC
TEKFEYDELKETLAKYNINMDDVEKFDIKKGKLLVYVNGEEHKIPLKEIE
LSAGCKMCRDFDAEMADVSVGCVGSPDGYSTVIIRTEKGEEIKNAIELKE
GVNLEAIEKLRDLKLNRFKKEVERRKAEDEKVSFYWTADYGGVGKRADGT
YFIRIRAKPAGWYSIDEAREILEIAEKYDGKIKMTNRGAFEIHGISGFDV
EAMVLELMEKGFITGSEGPLVRATLACPGEGNCGSGLINTTELCKILEDN
FKEHPAPYKFKIAISGCPNKCVRPQIHDIGIAGVKFPVVNEENCNGCGRC
AEVCKIEAIDIRGETSYTNYNVCIGCGKCIKACPNEGRDVKEEGFMVYVG
GKTGREVIEGVSMKLMSVEEILNLIDKVLIVYHKYAKKPQRERLAAVMAR
IGKGKFLEEVKELMEQN
Ligand information
Ligand IDFAD
InChIInChI=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
InChIKeyVWWQXMAJTJZDQX-UYBVJOGSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc2N=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 1.5.0Cc1cc2c(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 1.5.0Cc1cc2c(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 3.341Cc1cc2N=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 10.04O=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
FormulaC27 H33 N9 O15 P2
NameFLAVIN-ADENINE DINUCLEOTIDE
ChEMBLCHEMBL1232653
DrugBankDB03147
ZINCZINC000008215434
PDB chain7npa Chain D Residue 4607 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB7npa Structures of the sulfite detoxifying F 420 -dependent enzyme from Methanococcales.
Resolution1.55 Å
Binding residue
(original residue number in PDB)		G83 Q84 D85 G87 V88 V89 T90 V107 V108 T129 K131 S132 K133 Y134 S137 L158 L199 L200 C201 T202 E203 G272 C273 V274 S281
Binding residue
(residue number reindexed from 1)		G82 Q83 D84 G86 V87 V88 T89 V106 V107 T128 K130 S131 K132 Y133 S136 L157 L198 L199 C200 T201 E202 G271 C272 V273 S280
Annotation score1
Enzymatic activity
Enzyme Commision number 1.8.98.3: sulfite reductase (coenzyme F420).
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0016491 oxidoreductase activity
GO:0020037 heme binding
GO:0046872 metal ion binding
GO:0051536 iron-sulfur cluster binding
GO:0051539 4 iron, 4 sulfur cluster binding
GO:0052592 oxidoreductase activity, acting on CH or CH2 groups, with an iron-sulfur protein as acceptor

View graph for
Molecular Function
External links
PDB RCSB:7npa, PDBe:7npa, PDBj:7npa
PDBsum7npa
PubMed36658338
UniProtA0A2Z5PF12

[Back to BioLiP]