Structure of PDB 4k2s Chain A Binding Site BS01

Receptor Information
>4k2s Chain A (length=393) Species: 290398 (Chromohalobacter israelensis DSM 3043) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLKIRDAYTIVTCPGRNFVTLKIVTESGTHGIGDATLNGREMAVAAYLDE
HVVPALIGRDAGRIEDTWQYLYRGAYWRRGPVTMTAIAAVDMALWDIKAK
AAGMPLYQLLGGKSRERVMTYAHCTGQTIEDCLGEVARHVELGYRAVRVQ
SGVPGIETTYGVASSLPAEHVWSTEKYLNHAPKLFAAVRERFGDDLHVLH
DVHHRLTPIEAARLGKAVEPYHLFWLEDCVPAENQESLRLIREHTTTPLA
IGEVFNSIHDCRELIQNQWIDYIRMPLTHGGGITAMRRVADLASLYHVRT
GFHGATDLSPVCLGAAIHFDTWVPNFGIQEHMPHTDETDAVFPHDYRFED
GHFLAGESPGHGVDIDEELAAKYPYERASLPVNRLEDGTLWHW
Ligand information
Ligand IDGCO
InChIInChI=1S/C6H12O7/c7-1-2(8)3(9)4(10)5(11)6(12)13/h2-5,7-11H,1H2,(H,12,13)/t2-,3-,4+,5-/m1/s1
InChIKeyRGHNJXZEOKUKBD-SQOUGZDYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C([C@H]([C@H]([C@@H]([C@H](C(=O)O)O)O)O)O)O
OpenEye OEToolkits 1.5.0C(C(C(C(C(C(=O)O)O)O)O)O)O
CACTVS 3.341OC[CH](O)[CH](O)[CH](O)[CH](O)C(O)=O
CACTVS 3.341OC[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)C(O)=O
ACDLabs 10.04O=C(O)C(O)C(O)C(O)C(O)CO
FormulaC6 H12 O7
NameD-gluconic acid;
GLUCONIC ACID
ChEMBLCHEMBL464345
DrugBankDB13180
ZINCZINC000001531008
PDB chain4k2s Chain A 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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PDB4k2s Crystal structure of the mutant P317A of d-mannonate dehydratase from chromohalobacter salexigens complexed with mg and d-gluconate
Resolution1.699 Å
Binding residue
(original residue number in PDB)		N39 Y161 D213 H215 E265 H315 D319 E342
Binding residue
(residue number reindexed from 1)		N38 Y160 D201 H203 E253 H303 D307 E330
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) H124 R149 Q151 Y161 D213 H215 E239 G264 E265 R286 P288 H315 G316 E342 W405
Catalytic site (residue number reindexed from 1) H123 R148 Q150 Y160 D201 H203 E227 G252 E253 R274 P276 H303 G304 E330 W393
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:4k2s, PDBe:4k2s, PDBj:4k2s
PDBsum4k2s
PubMed
UniProtQ1QT89|DMGD_CHRSD D-galactonate dehydratase family member ManD (Gene Name=manD)

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