Structure of PDB 2ezt Chain B Binding Site BS02

Receptor Information

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

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

Ligand information

• Ligand ID: TDM
• InChI: InChI=1S/C14H22N4O8P2S/c1-8-12(4-5-25-28(23,24)26-27(20,21)22)29-14(9(2)19)18(8)7-11-6-16-10(3)17-13(11)15/h6,19H,4-5,7H2,1-3H3,(H,23,24)(H2,15,16,17)(H2,20,21,22)/b14-9+
• InChIKey: ZZLCKFKIIVXBQU-NTEUORMPSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: Cc1ncc(c(n1)N)CN\2C(=C(S/C2=C(\C)/O)CCO[P@@](=O)(O)OP(=O)(O)O)C
  CACTVS 3.341: C\C(O)=C1/SC(=C(C)N1Cc2cnc(C)nc2N)CCO[P@](O)(=O)O[P](O)(O)=O
  OpenEye OEToolkits 1.5.0: Cc1ncc(c(n1)N)CN2C(=C(SC2=C(C)O)CCOP(=O)(O)OP(=O)(O)O)C
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCCC=1S\C(=C(\O)C)N(C=1C)Cc2cnc(nc2N)C
  CACTVS 3.341: CC(O)=C1SC(=C(C)N1Cc2cnc(C)nc2N)CCO[P](O)(=O)O[P](O)(O)=O
• Formula: C14 H22 N4 O8 P2 S
• Name: 2-[(2E)-3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-(1-HYDROXYETHYLIDENE)-4-METHYL-2,3-DIHYDRO-1,3-THIAZOL-5-YL]ETHYL TRIHYDROGEN DIPHOSPHATE;
  2-HYDROXYETHYLTHIAMIN DIPHOSPHATE
• ZINC: ZINC000103557856
• PDB chain: 2ezt Chain B Residue 1614

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2ezt The catalytic cycle of a thiamin diphosphate enzyme examined by cryocrystallography.
• Resolution: 2.29 Å
• Binding residue (original residue number in PDB): V394 G395 D396 A420 M422 G446 D447 G448 N474 Q476 Y477 G478 W479 I480
• Binding residue (residue number reindexed from 1): V386 G387 D388 A412 M414 G438 D439 G440 N466 Q468 Y469 G470 W471 I472
• 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:2ezt, PDBe:2ezt, PDBj:2ezt
• PDBsum: 2ezt
• PubMed: 16680160
• UniProt: P37063|POXB_LACPL Pyruvate oxidase (Gene Name=pox5)