Structure of PDB 3eya Chain L Binding Site BS03

Receptor Information

>3eya Chain L (length=523) Species: 562 (Escherichia coli)

MKQTVAAYIAKTLESAGVKRIWGVTGDSLNGLSDSLNRMGTIEWMSTRHE
EVAAFAAGAEAQLSGELAVCAGSCGPGNLHLINGLFDCHRNHVPVLAIAA
HIPSSEIGSGYFQETHPQELFRECSHYCELVSSPEQIPQVLAIAMRKAVL
NRGVSVVVLPGDVALKPAPEGATMHWYHAPQPVVTPEEEELRKLAQLLRY
SSNIALMCGSGCAGAHKELVEFAGKIKAPIVHALRGKEHVEYDNPYDVGM
TGLIGFSSGFHTMMNADTLVLLGTQFPYRAFYPTDAKIIQIDINPASIGA
HSKVDMALVGDIKSTLRALLPLVEEKADRKFLDKALEDYRDARKGLDDLA
KPSEKAIHPQYLAQQISHFAADDAIFTCDVGTPTVWAARYLKMNGKRRLL
GSFNHGSMANAMPQALGAQATEPERQVVAMCGDGGFSMLMGDFLSVVQMK
LPVKIVVFNNSVLGFVGTELHDTNFARIAEACGITGIRVEKASEVDEALQ
RAFSIDGPVLVDVVVAKEELAIP

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: 3eya Chain L Residue 612

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3eya Structural basis for membrane binding and catalytic activation of the peripheral membrane enzyme pyruvate oxidase from Escherichia coli.
• Resolution: 2.5 Å
• Binding residue (original residue number in PDB): H92 G209 S210 G211 A233 L234 R235 T251 G252 I254 G273 T274 Q275 F276 Y278 D292 I293 S297 D311 I312 F403 N404
• Binding residue (residue number reindexed from 1): H92 G209 S210 G211 A233 L234 R235 T251 G252 I254 G273 T274 Q275 F276 Y278 D292 I293 S297 D311 I312 F403 N404
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): V24 G26 D27 S28 L29 E50 S73 F112 Q113 G161 L253 A280 V380 G406 M408 D433 N460 V462 L463 F465 V466 K529
• Catalytic site (residue number reindexed from 1): V24 G26 D27 S28 L29 E50 S73 F112 Q113 G161 L253 A280 V380 G406 M408 D433 N460 V462 L463 F465 V466 K517
• Enzyme Commision number: 1.2.5.1: pyruvate dehydrogenase (quinone).

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0000287 magnesium ion binding
• GO:0003824 catalytic activity
• GO:0008289 lipid binding
• GO:0016491 oxidoreductase activity
• GO:0030976 thiamine pyrophosphate binding
• GO:0042802 identical protein binding
• GO:0046872 metal ion binding
• GO:0048039 ubiquinone binding
• GO:0050660 flavin adenine dinucleotide binding
• GO:0052737 pyruvate dehydrogenase (quinone) activity

Biological Process

• GO:0006090 pyruvate metabolic process
• GO:0019752 carboxylic acid metabolic process
• GO:0042867 pyruvate catabolic process

Cellular Component

• GO:0005829 cytosol
• GO:0005886 plasma membrane
• GO:0032991 protein-containing complex

External links

• PDB: RCSB:3eya, PDBe:3eya, PDBj:3eya
• PDBsum: 3eya
• PubMed: 18988747
• UniProt: P07003|POXB_ECOLI Pyruvate dehydrogenase [ubiquinone] (Gene Name=poxB)