Structure of PDB 1m5w Chain B Binding Site BS01

Receptor Information
>1m5w Chain B (length=242) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AELLLGVNIDHIATLRNARGTAYPDPVQAAFIAEQAGADGITVHLREDRR
HITDRDVRILRQTLDTRMNLEMAVTEEMLAIAVETKPHFCCLVPEKRQEV
TTEGGLDVAGQRDKMRDACKRLADAGIQVSLFIDADEEQIKAAAEVGAPF
IEIHTGCYADAKTDAEQAQELARIAKAATFAASLGLKVNAGHGLTYHNVK
AIAAIPEMHELNIGHAIIGRAVMTGLKDAVAEMKRLMLEARG
Ligand information
Ligand IDDXP
InChIInChI=1S/C5H11O7P/c1-3(6)5(8)4(7)2-12-13(9,10)11/h4-5,7-8H,2H2,1H3,(H2,9,10,11)/t4-,5-/m1/s1
InChIKeyAJPADPZSRRUGHI-RFZPGFLSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(=O)[C@H]([C@@H](COP(=O)(O)O)O)O
OpenEye OEToolkits 1.5.0CC(=O)C(C(COP(=O)(O)O)O)O
CACTVS 3.341CC(=O)[CH](O)[CH](O)CO[P](O)(O)=O
CACTVS 3.341CC(=O)[C@@H](O)[C@H](O)CO[P](O)(O)=O
ACDLabs 10.04O=P(O)(O)OCC(O)C(O)C(=O)C
FormulaC5 H11 O7 P
Name1-DEOXY-D-XYLULOSE-5-PHOSPHATE
ChEMBLCHEMBL1232414
DrugBankDB02496
ZINC
PDB chain1m5w Chain B Residue 1002 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1m5w Multistate Binding in Pyridoxine 5'-Phosphate Synthase: 1.96 A Crystal Structure in Complex with 1-deoxy-D-xylulose phosphate
Resolution1.96 Å
Binding residue
(original residue number in PDB)		N9 D11 H52 G215 H216
Binding residue
(residue number reindexed from 1)		N8 D10 H51 G214 H215
Annotation score5
Binding affinityMOAD: Kd=54uM
Enzymatic activity
Catalytic site (original residue number in PDB) N9 H12 H45 R47 R51 E72 T103 E153 H193
Catalytic site (residue number reindexed from 1) N8 H11 H44 R46 R50 E71 T102 E152 H192
Enzyme Commision number 2.6.99.2: pyridoxine 5'-phosphate synthase.
Gene Ontology
Molecular Function
GO:0016740 transferase activity
GO:0016769 transferase activity, transferring nitrogenous groups
GO:0033856 pyridoxine 5'-phosphate synthase activity
GO:0042802 identical protein binding
Biological Process
GO:0008615 pyridoxine 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:1m5w, PDBe:1m5w, PDBj:1m5w
PDBsum1m5w
PubMed12269807
UniProtP0A794|PDXJ_ECOLI Pyridoxine 5'-phosphate synthase (Gene Name=pdxJ)

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