Structure of PDB 3twb Chain D Binding Site BS02

Receptor Information
>3twb Chain D (length=416) Species: 550537 (Salmonella enterica subsp. enterica serovar Enteritidis str. P125109) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SNLKITNVKTILTAPGGIDLAVVKIETNEPGLYGLGCATFTQRIFAVKSA
IDEYMAPFLVGKDPTRIEDIWQSGVVSGYWRNGPIMNNALSGVDMALWDI
KGKLAGMPVYDLLGGKCRDGIPLYCHTDGGDEVEVEDNIRARMEEGYQYV
RCQMGMYGGAGTDDLKLIATQLARAKNIQPKRSPRSKTPGIYFDPDAYAK
SVPRLFDHLRNKLGFGIEFIHDVHERVTPVTAINLAKTLEQYQLFYLEDP
VAPENIDWLKMLRQQSSTPISMGELFVNVNEWKPLIDNRLIDYIRCHVST
IGGITPARKLAVYSELNGVRTAWHGPGDISPVGVCANMHLDLSSPNFGIQ
EYTPMNDALRDVFPGCPEIDHGYAYLNDKPGLGIDIDEAKAAKYPCEGGI
PSWTMARTPDGTASRP
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 chain3twb Chain D Residue 422 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3twb Crystal Structure of Gluconate Dehydratase from Salmonella Enterica P125109
Resolution1.76 Å
Binding residue
(original residue number in PDB)		R154 Y160 D225 H227 E277 H327 P329 D331 E354
Binding residue
(residue number reindexed from 1)		R151 Y157 D222 H224 E274 H324 P326 D328 E351
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) F43 R46 P125 R154 Q156 D166 D225 H227 E251 G276 E277 L278 R298 H300 H327 P329 E354 P419
Catalytic site (residue number reindexed from 1) F40 R43 P122 R151 Q153 D163 D222 H224 E248 G273 E274 L275 R295 H297 H324 P326 E351 P416
Enzyme Commision number 4.2.1.-
4.2.1.39: gluconate dehydratase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
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:3twb, PDBe:3twb, PDBj:3twb
PDBsum3twb
PubMed
UniProtB5R541|DGD_SALEP D-galactonate dehydratase family member SEN1436 (Gene Name=SEN1436)

[Back to BioLiP]