Structure of PDB 3dbn Chain A Binding Site BS02

Receptor Information
>3dbn Chain A (length=349) Species: 391295 (Streptococcus suis 05ZYH33) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SHMKMSFRWYGKKDPVTLEEIKAIPGMQGIVTAVYDVPVGQAWPLENILE
LKKMVEEAGLEITVIESIPVHEDIKQGKPNRDALIENYKTSIRNVGAAGI
PVVCYNFMPVFDWTRSDLHHPLPDGSTSLAFLKSDLAGVDPSKEEMKAII
ENYRQNISEEDLWANLEYFIKAILPTAEEAGVKMAIHPDDPPYGIFGLPR
IITGQEAVERFLNLYDSEHNGITMCVGSYASDPKNDVLAMTEYALKRNRI
NFMHTRNVTAGAWGFQETAHLSQAGDIDMNAVVKLLVDYDWQGSLRPDHG
RRIWGDQTKTPGYGLYDRALGATYFNGLYEANMRAAGKTPDFGIKAKTV
Ligand information
Ligand IDCS2
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-MBMOQRBOSA-N
SMILES
SoftwareSMILES
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
OpenEye OEToolkits 1.5.0C([C@H]([C@H]([C@@H]([C@@H](C(=O)O)O)O)O)O)O
ACDLabs 10.04O=C(O)C(O)C(O)C(O)C(O)CO
CACTVS 3.341OC[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)C(O)=O
FormulaC6 H12 O7
NameD-MANNONIC ACID;
D-MANNONATE
ChEMBL
DrugBank
ZINCZINC000002040884
PDB chain3dbn Chain A Residue 388 [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]
PDB3dbn Crystal structures of Streptococcus suis mannonate dehydratase (ManD) and its complex with substrate: genetic and biochemical evidence for a catalytic mechanism
Resolution2.9 Å
Binding residue
(original residue number in PDB)		R26 W131 H219 D330 H331 P343 Y345
Binding residue
(residue number reindexed from 1)		R8 W113 H187 D298 H299 P311 Y313
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) H219 C257 H286 D330 H331 Y345
Catalytic site (residue number reindexed from 1) H187 C225 H254 D298 H299 Y313
Enzyme Commision number 4.2.1.8: mannonate dehydratase.
Gene Ontology
Molecular Function
GO:0008198 ferrous iron binding
GO:0008927 mannonate dehydratase activity
GO:0016829 lyase activity
GO:0030145 manganese ion binding
Biological Process
GO:0006064 glucuronate catabolic process
GO:0042840 D-glucuronate catabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3dbn, PDBe:3dbn, PDBj:3dbn
PDBsum3dbn
PubMed19617363
UniProtA4VVI4|UXUA_STRSY Mannonate dehydratase (Gene Name=uxuA)

[Back to BioLiP]