Structure of PDB 5xmj Chain A Binding Site BS01

Receptor Information
>5xmj Chain A (length=622) Species: 879 (Megalodesulfovibrio gigas) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MQIYHTDVLCIGGALAGERVAVEASMAGLKTIMLSLVPPRRSHSSAAQGG
MQAALGNAIMGDGDSPDVHFADTVKGSDWGCDQEVARIFADTAPIVMREV
AHWGVPWNRVVPGKHTYYKGGKPFEAEEKAEKAGLIHARAFGGTAAWRTC
YTADGTGRSVLNTLDTKCLQYGVTVHDRMQAEALIHDGGNCLGCIARCLR
TGELVAYLATSTLIATGGYGRIYKATTNAVICDGGGQIIALDTGLVPMGN
MEAVQFHPTGTVPTDILVTEGCRGDGGTLLDVNQYRFMPDYEPDKAQLAS
RDVVSRRMTEHMRKGLGVKSPYGDHLWLDIRHLGEKHITTKLREVYDICT
NFLGVNPIHQLIPVRPTHHYSMGGVRTNRDGAAYGLKGLFSAGESACWDM
HGFNRLGGNSLAETVVAGRYIGERMVEFTKGATPSFGMQYVEDAHKKVQE
RITDIVTGRKGKENTFKIRDEMHDIMMEGVGIFRNGTDLQKAVNKLEELY
DRSQKISLSSACKGMNPELSTALRIRGMLKLAQCTAYGALDRTESRGAHT
REDFPERNDKEWLNRTLSYWKEGASMPTLEYEEASPYYEMPPGDRGYGGG
VTIANELPPEKFVIPEAAKENL
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 chain5xmj Chain A Residue 701 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5xmj Structural insights into the electron/proton transfer pathways in the quinol:fumarate reductase from Desulfovibrio gigas.
Resolution3.6 Å
Binding residue
(original residue number in PDB)		G12 G13 A14 L36 S42 H43 S44 A46 A47 G49 A181 A215 T216 T227 N228 H369 E394 R405 G408 S410 L411
Binding residue
(residue number reindexed from 1)		G12 G13 A14 L36 S42 H43 S44 A46 A47 G49 A181 A215 T216 T227 N228 H369 E394 R405 G408 S410 L411
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) F141 Q255 H257 L267 E270 R273 R301 H369 Y370 R405
Catalytic site (residue number reindexed from 1) F141 Q255 H257 L267 E270 R273 R301 H369 Y370 R405
Enzyme Commision number 1.3.5.1: succinate dehydrogenase.
Gene Ontology
Molecular Function
GO:0000104 succinate dehydrogenase activity
GO:0000166 nucleotide binding
GO:0009055 electron transfer activity
GO:0016491 oxidoreductase activity
GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors
GO:0050660 flavin adenine dinucleotide binding
Biological Process
GO:0009061 anaerobic respiration
GO:0022900 electron transport chain
Cellular Component
GO:0005886 plasma membrane
GO:0016020 membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5xmj, PDBe:5xmj, PDBj:5xmj
PDBsum5xmj
PubMed30297797
UniProtT2GB49

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