Structure of PDB 2ez4 Chain B Binding Site BS04

Receptor Information

>2ez4 Chain B (length=585) Species: 1590 (Lactiplantibacillus plantarum)

TNILAGAAVIKVLEAWGVDHLYGIPGGSINSIMDALSAERDRIHYIQVRH
EEVGAMAAAADAKLTGKIGVCFGSAGPGGTHLMNGLYDAREDHVPVLALI
GQFGTTGMNMDTFQEMNENPIYADVADYNVTAVNAATLPHVIDEAIRRAY
AHQGVAVVQIPVDLPWQQIPAEDWYASANSYQTPLLPEPDVQAVTRLTQT
LLAAERPLIYYGIGARKAGKELEQLSKTLKIPLMSTYPAKGIVADRYPAY
LGSANRVAQKPANEALAQADVVLFVGNNYPFAEVSKAFKNTRYFLQIDID
PAKLGKRHKTDIAVLADAQKTLAAILAQVSERESTPWWQANLANVKNWRA
YLASLEDKQEGPLQAYQVLRAVNKIAEPDAIYSIDVGDINLNANRHLKLT
PSNRHITSNLFATMGVGIPGAIAAKLNYPERQVFNLAGDGGASMTMQDLA
TQVQYHLPVINVVFTNCQYGWIKDEQEDTNQNDFIGVEFNDIDFSKIADG
VHMQAFRVNKIEQLPDVFEQAKAIAQHEPVLIDAVITGDRPLPAEKLRLD
SAMSSAADIEAFKQRYEAQDLQPLSTYLKQFGLDD

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: 2ez4 Chain B Residue 1619

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2ez4 The catalytic cycle of a thiamin diphosphate enzyme examined by cryocrystallography.
• Resolution: 2.03 Å
• Binding residue (original residue number in PDB): H101 G220 I221 G222 T244 Y245 P246 A262 N263 R264 V265 G284 N285 N286 P288 F289 D306 I307 K311 D325 A326 N417
• Binding residue (residue number reindexed from 1): H93 G212 I213 G214 T236 Y237 P238 A254 N255 R256 V257 G276 N277 N278 P280 F281 D298 I299 K303 D317 A318 N409
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): I32 G34 G35 S36 I37 E59 S82 F121 Q122 E123 V170 R264 E291 V394 A420 M422 D447 N474 Q476 Y477 W479 I480 E483 G546
• Catalytic site (residue number reindexed from 1): I24 G26 G27 S28 I29 E51 S74 F113 Q114 E115 V162 R256 E283 V386 A412 M414 D439 N466 Q468 Y469 W471 I472 E475 G538
• Enzyme Commision number: 1.2.3.3: pyruvate oxidase.

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0003824 catalytic activity
• GO:0016491 oxidoreductase activity
• GO:0030976 thiamine pyrophosphate binding
• GO:0046872 metal ion binding
• GO:0047112 pyruvate oxidase activity

External links

• PDB: RCSB:2ez4, PDBe:2ez4, PDBj:2ez4
• PDBsum: 2ez4
• PubMed: 16680160
• UniProt: P37063|POXB_LACPL Pyruvate oxidase (Gene Name=pox5)