Structure of PDB 2ez9 Chain B Binding Site BS02

Receptor Information

>2ez9 Chain B (length=585) Species: 1590 (Lactiplantibacillus plantarum)

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

Ligand information

• Ligand ID: TDK
• InChI: InChI=1S/C15H25N4O11P3S/c1-9-12(5-6-29-33(26,27)30-32(23,24)25)34-14(15(3,20)31(21,22)28-4)19(9)8-11-7-17-10(2)18-13(11)16/h7,20H,5-6,8H2,1-4H3,(H5-,16,17,18,21,22,23,24,25,26,27)/p+1/t15-/m0/s1
• InChIKey: ILGXNMPRCMTAOK-HNNXBMFYSA-O
• SMILES:
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCCc1sc([n+](c1C)Cc2cnc(nc2N)C)C(O)(P(=O)(OC)O)C
  OpenEye OEToolkits 1.7.5: Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(C)(O)P(=O)(O)OC)CCOP(=O)(O)OP(=O)(O)O
  OpenEye OEToolkits 1.7.5: Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@@](C)(O)[P@@](=O)(O)OC)CCO[P@@](=O)(O)OP(=O)(O)O
  CACTVS 3.385: CO[P](O)(=O)[C](C)(O)c1sc(CCO[P](O)(=O)O[P](O)(O)=O)c(C)[n+]1Cc2cnc(C)nc2N
  CACTVS 3.385: CO[P](O)(=O)[C@](C)(O)c1sc(CCO[P](O)(=O)O[P](O)(O)=O)c(C)[n+]1Cc2cnc(C)nc2N
• Formula: C15 H26 N4 O11 P3 S
• Name: 3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-{(1S)-1-HYDROXY-1-[(R)-HYDROXY(METHOXY)PHOSPHORYL]ETHYL}-5-(2-{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM;
  2-PHOSPHONOLACTYLTHIAMIN DIPHOSPHATE
• ZINC: ZINC000016051991
• PDB chain: 2ez9 Chain B Residue 1613

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2ez9 The catalytic cycle of a thiamin diphosphate enzyme examined by cryocrystallography.
• Resolution: 1.6 Å
• Binding residue (original residue number in PDB): V394 D396 M422 G446 G448 N474 Q476 Y477 G478 W479 I480 E483
• Binding residue (residue number reindexed from 1): V386 D388 M414 G438 G440 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:2ez9, PDBe:2ez9, PDBj:2ez9
• PDBsum: 2ez9
• PubMed: 16680160
• UniProt: P37063|POXB_LACPL Pyruvate oxidase (Gene Name=pox5)