Structure of PDB 4jdr Chain B Binding Site BS01

Receptor Information

>4jdr Chain B (length=471) Species: 562 (Escherichia coli)

STEIKTQVVVLGAGPAGYSAAFRCADLGLETVIVERYNTLGGVCLNVGCI
PSKALLHVAKVIEEAKALAEHGIVFGEPKTDIDKIRTWKEKVINQLTGGL
AGMAKGRKVKVVNGLGKFTGANTLEVEGENGKTVINFDNAIIAAGSRPIQ
LPFIPHEDPRIWDSTDALELKEVPERLLVMGGGIIGLEMGTVYHALGSQI
DVVEMFDQVIPAADKDIVKVFTKRISKKFNLMLETKVTAVEAKEDGIYVT
MEGKKAPAEPQRYDAVLVAIGRVPNGKNLDAGKAGVEVDDRGFIRVDKQL
RTNVPHIFAIGDIVGQPMLAHKGVHEGHVAAEVIAGKKHYFDPKVIPSIA
YTEPEVAWVGLTEKEAKEKGISYETATFPWAASGRAIASDCADGMTKLIF
DKESHRVIGGAIVGTNGGELLGEIGLAIEMGCDAEDIALTIHAHPTLHES
VGLAAEVFEGSITDLPNPKAK

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: 4jdr Chain B Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4jdr Insight to the Interaction of the Dihydrolipoamide Acetyltransferase (E2) Core with the Peripheral Components in the Escherichia coli Pyruvate Dehydrogenase Complex via Multifaceted Structural Approaches.
• Resolution: 2.5 Å
• Binding residue (original residue number in PDB): G13 G15 P16 A17 E36 R37 Y38 V44 C45 G49 C50 K54 L116 G117 A145 G146 I186 G312 D313 M319 L320 A321 H322
• Binding residue (residue number reindexed from 1): G12 G14 P15 A16 E35 R36 Y37 V43 C44 G48 C49 K53 L115 G116 A144 G145 I185 G311 D312 M318 L319 A320 H321
• Annotation score: 2

Enzymatic activity

• Catalytic site (original residue number in PDB): P16 L41 C45 C50 S53 E78 P79 I185 E189 V325 H443 H445 E450 N468 P469
• Catalytic site (residue number reindexed from 1): P15 L40 C44 C49 S52 E77 P78 I184 E188 V324 H442 H444 E449 N467 P468
• Enzyme Commision number: 1.8.1.4: dihydrolipoyl dehydrogenase.

Gene Ontology

Molecular Function

• GO:0004148 dihydrolipoyl dehydrogenase activity
• GO:0005515 protein binding
• GO:0008270 zinc ion binding
• GO:0015036 disulfide oxidoreductase activity
• GO:0016491 oxidoreductase activity
• GO:0016668 oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor
• GO:0042802 identical protein binding
• GO:0050660 flavin adenine dinucleotide binding

Biological Process

• GO:0006090 pyruvate metabolic process
• GO:0006099 tricarboxylic acid cycle
• GO:0006103 2-oxoglutarate metabolic process
• GO:0006730 one-carbon metabolic process
• GO:0006979 response to oxidative stress
• GO:0019464 glycine decarboxylation via glycine cleavage system
• GO:0042867 pyruvate catabolic process

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005886 plasma membrane
• GO:0005960 glycine cleavage complex
• GO:0016020 membrane
• GO:0045252 oxoglutarate dehydrogenase complex
• GO:0045254 pyruvate dehydrogenase complex

External links

• PDB: RCSB:4jdr, PDBe:4jdr, PDBj:4jdr
• PDBsum: 4jdr
• PubMed: 23580650
• UniProt: P0A9P0|DLDH_ECOLI Dihydrolipoyl dehydrogenase (Gene Name=lpdA)