Structure of PDB 2ixl Chain D Binding Site BS01

Receptor Information
>2ixl Chain D (length=196) Species: 1307 (Streptococcus suis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TENFFGKTLAARPVEAIPGMLEFDIPVHGDNRGWFKENFQKEKMLPLGFP
ESFFAEGKLQNNVSFSRKNVLRGLHAEPWDKYISVADGGKVLGTWVDLRE
GETFGNTYQTVIDASKSIFVPRGVANGFQVLSDFVAYSYLVNDYWALELK
PKYAFVNYADPSLDIKWENLEEAEVSEADENHPFLKDVKPLRKEDL
Ligand information
Ligand IDTRH
InChIInChI=1S/C16H26N2O15P2/c1-6-4-18(16(24)17-14(6)23)10-3-8(19)9(31-10)5-29-34(25,26)33-35(27,28)32-15-13(22)12(21)11(20)7(2)30-15/h4,7-13,15,19-22H,3,5H2,1-2H3,(H,25,26)(H,27,28)(H,17,23,24)/t7-,8-,9+,10+,11-,12+,13+,15+/m0/s1
InChIKeyZOSQFDVXNQFKBY-CGAXJHMRSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1C(C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(CC(O2)N3C=C(C(=O)NC3=O)C)O)O)O)O
CACTVS 3.341C[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH](C[CH]2O)N3C=C(C)C(=O)NC3=O)[CH](O)[CH](O)[CH]1O
CACTVS 3.341C[C@@H]1O[C@H](O[P@@](O)(=O)O[P@](O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N3C=C(C)C(=O)NC3=O)[C@H](O)[C@H](O)[C@H]1O
ACDLabs 10.04O=P(OC1OC(C(O)C(O)C1O)C)(O)OP(=O)(O)OCC3OC(N2C=C(C(=O)NC2=O)C)CC3O
OpenEye OEToolkits 1.5.0C[C@H]1[C@@H]([C@H]([C@H]([C@H](O1)O[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]2[C@H](C[C@@H](O2)N3C=C(C(=O)NC3=O)C)O)O)O)O
FormulaC16 H26 N2 O15 P2
Name2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE
ChEMBL
DrugBankDB03723
ZINCZINC000008218444
PDB chain2ixl Chain D Residue 1198 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2ixl Rmlc, a C3' and C5' Carbohydrate Epimerase, Appears to Operate Via an Intermediate with an Unusual Twist Boat Conformation.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		R73 H76 E78 K82 N127 Y140 W146
Binding residue
(residue number reindexed from 1)		R72 H75 E77 K81 N126 Y139 W145
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) H76 K82 Y140 D180
Catalytic site (residue number reindexed from 1) H75 K81 Y139 D179
Enzyme Commision number 5.1.3.13: dTDP-4-dehydrorhamnose 3,5-epimerase.
Gene Ontology
Molecular Function
GO:0008830 dTDP-4-dehydrorhamnose 3,5-epimerase activity
GO:0016853 isomerase activity
Biological Process
GO:0019305 dTDP-rhamnose biosynthetic process
GO:0045226 extracellular polysaccharide biosynthetic process
Cellular Component
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:2ixl, PDBe:2ixl, PDBj:2ixl
PDBsum2ixl
PubMed17046787
UniProtQ8GIQ0

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