Structure of PDB 5odi Chain A Binding Site BS01

Receptor Information
>5odi Chain A (length=651) Species: 523845 (Methanothermococcus thermolithotrophicus DSM 2095) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EPRIGVYVCHCGVNIGGTVDCPDVTEFAKTLKNVVVARDYKYMCADPGQE
MIKKDIKEHNLNRVVVAACSPRLHEPTFRRCVAEAGLNPFLFEFANIREH
CSWVHMHEKEKATEKAKDLVRMAVAKARLLEPLEFIKVGVTQRALVIGGG
VAGIQTALDLGDMGFETILVEKTPSVGGRMAQLDKTFPTNDCSICILAPK
MVDVAKHPNVKLYAYSEVVDVQGYVGNFKVKIMKKARYIDETKCTGCGQC
SEVCPIDVPNEFDMGIGMRKAIYKPFPQAVPAKYTIDKEHCIECGLCAKV
CGPNAIDFDQEPEIIEAEVGTIICAIGYDAFDPTVREEYGYGVYDNVVTA
LELERMINASGPTGGKVIRLSDGQKPKRIAFIQCVGSRDAKVGNKYCSNV
CCMYAMKNSQLIKEKSPDTEIDIYYMDIRAFSKGYEEFYERSAKQYGIKF
MRGRPSQVIEDPETGNLVVRAEDTLLGEILEKEYDLVVLSVGMVPTKSAD
EVQKILGISRTPDQFFMEAHPKLRPVDTATDGVYLAGACQGPKDIPASVA
QGSAAASRAAIPLAKGEVEVEPIIASVDAEICGGCGVCVKQCPYGAPRLV
EKDGKVVAEVISALCKGCGTCPAGCPSGALEQDHFKTIQLFKQIEGMFRD
T
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 chain5odi Chain A Residue 702 [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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PDB5odi Methanogenic heterodisulfide reductase (HdrABC-MvhAGD) uses two noncubane [4Fe-4S] clusters for reduction.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		I149 G150 G151 G152 V153 A154 E173 K174 G180 R181 L185 F189 A327 I328 G329 Y330 L353 Y406 K409 S500 D546 I547
Binding residue
(residue number reindexed from 1)		I147 G148 G149 G150 V151 A152 E171 K172 G178 R179 L183 F187 A325 I326 G327 Y328 L351 Y404 K407 S498 D544 I545
Annotation score4
Enzymatic activity
Enzyme Commision number 1.8.-.-
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
GO:0051539 4 iron, 4 sulfur cluster binding

View graph for
Molecular Function
External links
PDB RCSB:5odi, PDBe:5odi, PDBj:5odi
PDBsum5odi
PubMed28818947
UniProtA0A2D0TCB9

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