Structure of PDB 4z1d Chain B Binding Site BS01

Receptor Information
>4z1d Chain B (length=256) Species: 85962 (Helicobacter pylori 26695) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KSVLIAGPCVIESLENLRSIATKLQPLANNERLDFYFKASFDKANRTSLE
SYRGPGLEKGLEMLQTIKEEFGYKILTDVHESYQASVAAKVADILQIPAF
LCRQTDLIVEVSQTNAIVNIKKGQFMNPKDMQYSVLKALKTRDKSIQSPT
YETALKNGVWLCERGSSFGYGNLVVDMRSLKIMREFAPVIFDATHSVQMP
SFAPILARAAAAVGIDGLFAETHVDPKNALSDGANMLKPDELEQLVTDML
KIQNLF
Ligand information
Ligand IDPEP
InChIInChI=1S/C3H5O6P/c1-2(3(4)5)9-10(6,7)8/h1H2,(H,4,5)(H2,6,7,8)
InChIKeyDTBNBXWJWCWCIK-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C=C(C(=O)O)OP(=O)(O)O
CACTVS 3.341OC(=O)C(=C)O[P](O)(O)=O
ACDLabs 10.04O=C(O)C(\OP(=O)(O)O)=C
FormulaC3 H5 O6 P
NamePHOSPHOENOLPYRUVATE
ChEMBLCHEMBL1235228
DrugBankDB01819
ZINCZINC000003870145
PDB chain4z1d Chain B Residue 300 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4z1d Identification of novel scaffolds for potential anti-Helicobacter pylori agents based on the crystal structure of H. pylori 3-deoxy-d-manno-octulosonate 8-phosphate synthase (HpKDO8PS).
Resolution1.65 Å
Binding residue
(original residue number in PDB)		K47 K52 Q105 P107 A108 K130 R173 H204
Binding residue
(residue number reindexed from 1)		K38 K43 Q96 P98 A99 K121 R164 H195
Annotation score5
Enzymatic activity
Enzyme Commision number 2.5.1.55: 3-deoxy-8-phosphooctulonate synthase.
Gene Ontology
Molecular Function
GO:0008676 3-deoxy-8-phosphooctulonate synthase activity
GO:0016740 transferase activity
Biological Process
GO:0009058 biosynthetic process
GO:0009103 lipopolysaccharide biosynthetic process
GO:0019294 keto-3-deoxy-D-manno-octulosonic acid biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4z1d, PDBe:4z1d, PDBj:4z1d
PDBsum4z1d
PubMed26649906
UniProtP56060|KDSA_HELPY 2-dehydro-3-deoxyphosphooctonate aldolase (Gene Name=kdsA)

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