Structure of PDB 4kpl Chain D Binding Site BS01

Receptor Information
>4kpl Chain D (length=384) Species: 290398 (Chromohalobacter israelensis DSM 3043) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LKIRDAYTIVTCPGRNFVTLKIVTESGTHGIGDATLNGREMAVAAYLDEH
VVPALIGRDAGRIEDTWQYLYRGAYWRRGPVTMTAIAAVDMALWDIKAKA
AGMPLYQLLGGKSRERVMTYAHCTGQTIEDCLGEVARHVELGYRAVRVQS
GVPGSSLPAEHVWSTEKYLNHAPKLFAAVRERFGDDLHVLHDVHHRLTPI
EAARLGKAVEPYHLFWLEDCVPAENQESLRLIREHTTTPLAIGEVFNSIH
DCRELIQNQWIDYIRMPLTHGGGITAMRRVADLASLYHVRTGFHGPTDLS
PVCLGAAIHFDTWVPNFGIQEHMPHTDETDAVFPHDYRFEDGHFLAGESP
GHGVDIDEELAAKYPYERASLPVNRLEDGTLWHW
Ligand information
Ligand IDKDG
InChIInChI=1S/C6H10O6/c7-2-5(10)3(8)1-4(9)6(11)12/h3,5,7-8,10H,1-2H2,(H,11,12)/t3-,5+/m0/s1
InChIKeyWPAMZTWLKIDIOP-WVZVXSGGSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C([C@@H]([C@@H](CO)O)O)C(=O)C(=O)O
CACTVS 3.341OC[C@@H](O)[C@@H](O)CC(=O)C(O)=O
ACDLabs 10.04O=C(C(=O)O)CC(O)C(O)CO
CACTVS 3.341OC[CH](O)[CH](O)CC(=O)C(O)=O
OpenEye OEToolkits 1.5.0C(C(C(CO)O)O)C(=O)C(=O)O
FormulaC6 H10 O6
Name2-KETO-3-DEOXYGLUCONATE
ChEMBL
DrugBank
ZINCZINC000001532568
PDB chain4kpl Chain D Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4kpl Crystal structure of d-mannonate dehydratase from chromohalobacter salexigens complexed with Mg,d-mannonate and 2-keto-3-deoxy-d-gluconate
Resolution2.0 Å
Binding residue
(original residue number in PDB)		N39 D213 H215 E265 H315 P317 D319 E342
Binding residue
(residue number reindexed from 1)		N37 D192 H194 E244 H294 P296 D298 E321
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) H124 R149 Q151 D213 H215 E239 G264 E265 R286 P288 H315 G316 E342 W405
Catalytic site (residue number reindexed from 1) H122 R147 Q149 D192 H194 E218 G243 E244 R265 P267 H294 G295 E321 W384
Enzyme Commision number 4.2.1.-
4.2.1.39: gluconate dehydratase.
4.2.1.8: mannonate dehydratase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0008927 mannonate dehydratase activity
GO:0016829 lyase activity
GO:0046872 metal ion binding
GO:0047929 gluconate dehydratase activity
Biological Process
GO:0009063 amino acid catabolic process
GO:0016052 carbohydrate catabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4kpl, PDBe:4kpl, PDBj:4kpl
PDBsum4kpl
PubMed
UniProtQ1QT89|DMGD_CHRSD D-galactonate dehydratase family member ManD (Gene Name=manD)

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