Structure of PDB 1nyw Chain B Binding Site BS02

Receptor Information
>1nyw Chain B (length=195) Species: 1307 (Streptococcus suis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ENFFGKTLAARPVEAIPGMLEFDIPVHGDNRGWFKENFQKEKMLPLGFPE
SFFAEGKLQNNVSFSRKNVLRGLHAEPWDKYISVADGGKVLGTWVDLREG
ETFGNTYQTVIDASKSIFVPRGVANGFQVLSDFVAYSYLVNDYWALELKP
KYAFVNYADPSLDIKWENLEEAEVSEADENHPFLKDVKPLRKEDL
Ligand information
Ligand IDDAU
InChIInChI=1S/C16H26N2O16P2/c1-6-3-18(16(25)17-14(6)24)10-2-7(20)9(31-10)5-30-35(26,27)34-36(28,29)33-15-13(23)12(22)11(21)8(4-19)32-15/h3,7-13,15,19-23H,2,4-5H2,1H3,(H,26,27)(H,28,29)(H,17,24,25)/t7-,8+,9+,10+,11+,12-,13+,15+/m0/s1
InChIKeyYSYKRGRSMLTJNL-URARBOGNSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[CH]3O[CH](CO)[CH](O)[CH](O)[CH]3O)O2)C(=O)NC1=O
OpenEye OEToolkits 1.7.6CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OC3C(C(C(C(O3)CO)O)O)O)O
CACTVS 3.370CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)O2)C(=O)NC1=O
OpenEye OEToolkits 1.7.6CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(O)O[P@](=O)(O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O)O
ACDLabs 12.01O=C1C(=CN(C(=O)N1)C2OC(C(O)C2)COP(=O)(OP(=O)(OC3OC(C(O)C(O)C3O)CO)O)O)C
FormulaC16 H26 N2 O16 P2
Name2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALPHA-D-GLUCOSE
ChEMBLCHEMBL412989
DrugBankDB03751
ZINC
PDB chain1nyw Chain B Residue 5001 [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]
PDB1nyw High-Resolution Structures of RmlC from Streptococcus suis in Complex with Substrate Analogs Locate the Active Site of This Class of Enzyme
Resolution1.6 Å
Binding residue
(original residue number in PDB)		S65 R73 E78 K82 Y140 W146
Binding residue
(residue number reindexed from 1)		S63 R71 E76 K80 Y138 W144
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) H76 K82 Y140 D180
Catalytic site (residue number reindexed from 1) H74 K80 Y138 D178
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1nyw, PDBe:1nyw, PDBj:1nyw
PDBsum1nyw
PubMed12791259
UniProtQ8GIQ0

[Back to BioLiP]