Structure of PDB 2wdq Chain E Binding Site BS01

Receptor Information

>2wdq Chain E (length=588) Species: 562 (Escherichia coli)

MKLPVREFDAVVIGAGGAGMRAALQISQSGQTCALLSKVFPTRSHTVSAQ
GGITVALGNTHEDNWEWHMYDTVKGSDYIGDQDAIEYMCKTGPEAILELE
HMGLPFSRLDDGRIYQRPFGGQSKNFGGEQAARTAAAADRTGHALLHTLY
QQNLKNHTTIFSEWYALDLVKNQDGAVVGCTALCIETGEVVYFKARATVL
ATGGAGRIYQSTTNAHINTGDGVGMAIRAGVPVQDMEMWQFHPTGIAGAG
VLVTEGCRGEGGYLLNKHGERFMERYAPNAKDLAGRDVVARSIMIEIREG
RGCDGPWGPHAKLKLDHLGKEVLESRLPGILELSRTFAHVDPVKEPIPVI
PTCHYMMGGIPTKVTGQALTVNEKGEDVVVPGLFAVGEIACVSVHGANRL
GGNSLLDLVVFGRAAGLHLQESIAEQGALRDASESDVEASLDRLNRWNNN
RNGEDPVAIRKALQECMQHNFSVFREGDAMAKGLEQLKVIRERLKNARLD
DTSSEFNTQRVECLELDNLMETAYATAVSANFRTESRGAHSRFDFPDRDD
ENWLCHSLYLPESESMTRRSVNMEPKLRPAFPPKIRTY

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: 2wdq Chain E Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2wdq Structure of Escherichia coli succinate:quinone oxidoreductase with an occupied and empty quinone-binding site.
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): G14 A15 G16 A18 S37 K38 V39 S44 H45 T46 S48 A49 Q50 G51 G52 Y165 A166 A201 T202 D221 L252 H354 Y355 E388 G402 S404 L405 L408
• Binding residue (residue number reindexed from 1): G14 A15 G16 A18 S37 K38 V39 S44 H45 T46 S48 A49 Q50 G51 G52 Y165 A166 A201 T202 D221 L252 H354 Y355 E388 G402 S404 L405 L408
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): F119 T213 W239 Q240 H242 L252 E255 R258 R286 L323 I347 H354 Y355 N398 R399
• Catalytic site (residue number reindexed from 1): F119 T213 W239 Q240 H242 L252 E255 R258 R286 L323 I347 H354 Y355 N398 R399
• Enzyme Commision number: 1.3.5.1: succinate dehydrogenase.

Gene Ontology

Molecular Function

• GO:0000104 succinate dehydrogenase activity
• 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

Biological Process

• GO:0006099 tricarboxylic acid cycle
• GO:0009060 aerobic respiration
• GO:0009061 anaerobic respiration
• GO:0019646 aerobic electron transport chain
• GO:0022900 electron transport chain

Cellular Component

• GO:0005886 plasma membrane
• GO:0016020 membrane
• GO:0045273 respiratory chain complex II (succinate dehydrogenase)

External links

• PDB: RCSB:2wdq, PDBe:2wdq, PDBj:2wdq
• PDBsum: 2wdq
• PubMed: 19710024
• UniProt: P0AC41|SDHA_ECOLI Succinate dehydrogenase flavoprotein subunit (Gene Name=sdhA)