Structure of PDB 2ez8 Chain B Binding Site BS02

Receptor Information

>2ez8 Chain B (length=585) Species: 1590 (Lactiplantibacillus plantarum)

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

Ligand information

• Ligand ID: TDL
• InChI: InChI=1S/C15H22N4O10P2S/c1-8-11(4-5-28-31(26,27)29-30(23,24)25)32-13(15(3,22)14(20)21)19(8)7-10-6-17-9(2)18-12(10)16/h6,22H,4-5,7H2,1-3H3,(H5-,16,17,18,20,21,23,24,25,26,27)/p+1/t15-/m1/s1
• InChIKey: TVDSMGSBVYONNB-OAHLLOKOSA-O
• SMILES:
  OpenEye OEToolkits 1.7.5: Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(C)(C(=O)O)O)CCOP(=O)(O)OP(=O)(O)O
  OpenEye OEToolkits 1.7.5: Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@](C)(C(=O)O)O)CCO[P@@](=O)(O)OP(=O)(O)O
  CACTVS 3.385: Cc1ncc(C[n+]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2[C](C)(O)C(O)=O)c(N)n1
  CACTVS 3.385: Cc1ncc(C[n+]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2[C@@](C)(O)C(O)=O)c(N)n1
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCCc1sc([n+](c1C)Cc2cnc(nc2N)C)C(O)(C(=O)O)C
• Formula: C15 H23 N4 O10 P2 S
• Name: 3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-(1-CARBOXY-1-HYDROXYETHYL)-5-(2-{[HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM;
  2-LACTYLTHIAMIN DIPHOSPHATE
• ZINC: ZINC000016051990
• PDB chain: 2ez8 Chain B Residue 1616

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2ez8 The catalytic cycle of a thiamin diphosphate enzyme examined by cryocrystallography.
• Resolution: 1.963 Å
• Binding residue (original residue number in PDB): V394 D396 M422 G446 G448 G449 N474 Q476 Y477 G478 W479 I480 E483
• Binding residue (residue number reindexed from 1): V386 D388 M414 G438 G440 G441 N466 Q468 Y469 G470 W471 I472 E475
• 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:2ez8, PDBe:2ez8, PDBj:2ez8
• PDBsum: 2ez8
• PubMed: 16680160
• UniProt: P37063|POXB_LACPL Pyruvate oxidase (Gene Name=pox5)