Structure of PDB 3p4s Chain M Binding Site BS01

Receptor Information

>3p4s Chain M (length=577) Species: 216592 (Escherichia coli 042)

MQTFQADLAIVGAGGAGLRAAIAAAQANPNAKIALISKVYPMRSHTVAAE
GGSAAVAQDHDSFEYHFHDTVAGGDWLCEQDVVDYFVHHCPTEMTQLELW
GCPWSRRPDGSVNVRRFGGMKIERTWFAADKTGFHMLHTLFQTSLQFPQI
QRFDEHFVLDILVDDGHVRGLVAMNMMEGTLVQIRANAVVMATGGAGRVY
RYNTNGGIVTGDGMGMALSHGVPLRDMEFVQYHPTGLPGSGILMTEGCRG
EGGILVNKNGYRYLQDYGMGPETPLGEPKNKYMELGPRDKVSQAFWHEWR
KGNTISTPRGDVVYLDLRHLGEKKLHERLPFICELAKAYVGVDPVKEPIP
VRPTAHYTMGGIETDQNCETRIKGLFAVGECSSVGLHGANRLGSNSLAEL
VVFGRLAGEQATERAATAGNGNEAAIEAQAAGVEQRLKDLVNQDGGENWA
KIRDEMGLAMEEGCGIYRTPELMQKTIDKLAELQERFKRVRITDTSSVFN
TDLLYTIELGHGLNVAECMAHSAMARKESRGAHQRLDEGCTERDDVNFLK
HTLAFRDADGTTRLEYSDVKITTLPPA

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: 3p4s Chain M Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3p4s Geometric restraint drives on- and off-pathway catalysis by the Escherichia coli menaquinol:fumarate reductase.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): V10 G11 A12 G13 S36 K37 V38 S43 H44 T45 A48 G50 G51 H155 V157 A191 T192 L242 H355 Y356 N394 S395 L396 L399
• Binding residue (residue number reindexed from 1): V11 G12 A13 G14 S37 K38 V39 S44 H45 T46 A49 G51 G52 H156 V158 A192 T193 L243 H356 Y357 N395 S396 L397 L400
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): F116 H232 R287 H355 Y356 R390
• Catalytic site (residue number reindexed from 1): F117 H233 R288 H356 Y357 R391
• Enzyme Commision number: 1.3.5.1: succinate dehydrogenase.

Gene Ontology

Molecular Function

• GO:0000104 succinate dehydrogenase activity
• GO:0000166 nucleotide binding
• GO:0005515 protein binding
• GO:0008177 succinate dehydrogenase (quinone) activity
• 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
• GO:0071949 FAD binding

Biological Process

• GO:0006113 fermentation
• GO:0006974 DNA damage response
• GO:0009061 anaerobic respiration
• GO:0019645 anaerobic electron transport chain
• GO:0022900 electron transport chain
• GO:0044780 bacterial-type flagellum assembly

Cellular Component

• GO:0005829 cytosol
• GO:0005886 plasma membrane
• GO:0016020 membrane
• GO:0045283 fumarate reductase complex

External links

• PDB: RCSB:3p4s, PDBe:3p4s, PDBj:3p4s
• PDBsum: 3p4s
• PubMed: 21098488
• UniProt: P00363|FRDA_ECOLI Fumarate reductase flavoprotein subunit (Gene Name=frdA)