Structure of PDB 3hdy Chain C Binding Site BS02

Receptor Information
>3hdy Chain C (length=349) Species: 1299 (Deinococcus radiodurans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LIVGAGFAGSVLAERLASSGQRVLIVDRRPHIGGNAYDCYDDAGVLIHPY
GPHIFHTNSKDVFEYLSRFTEWRPYQHRVLASVDGQLLPIPINLDTVNRL
YGLNLTSFQVEEFFASVAEKVEQVRTSEDVVVSKVGRDLYNKFFRGYTRK
QWGLDPSELDASVTARVPTRTNRDNRYFADTYQAMPLHGYTRMFQNMLSS
PNIKVMLNTDYREIADFIPFQHMIYTGPVDAFFDFCYGKLPYRSLEFRHE
THDTEQLLPTGTVNYPNDYAYTRVSEFKHITGQRHHQTSVVYEYPRAEGD
PYYPVPRPENAELYKKYEALADAAQDVTFVGRLATYRYYNMDQVVAQAL
Ligand information
Ligand IDGDU
InChIInChI=1S/C15H24N2O17P2/c18-3-5-8(20)10(22)12(24)14(32-5)33-36(28,29)34-35(26,27)30-4-6-9(21)11(23)13(31-6)17-2-1-7(19)16-15(17)25/h1-2,5-6,8-14,18,20-24H,3-4H2,(H,26,27)(H,28,29)(H,16,19,25)/t5-,6-,8+,9-,10+,11-,12-,13-,14-/m1/s1
InChIKeyHSCJRCZFDFQWRP-ABVWGUQPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([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)O
CACTVS 3.341OC[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH](O)[CH](O)[CH]1O
CACTVS 3.341OC[C@H]1O[C@H](O[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)[C@H](O)[C@@H](O)[C@H]1O
ACDLabs 10.04O=P(OC1OC(C(O)C(O)C1O)CO)(O)OP(=O)(O)OCC3OC(N2C=CC(=O)NC2=O)C(O)C3O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OC3C(C(C(C(O3)CO)O)O)O)O)O
FormulaC15 H24 N2 O17 P2
NameGALACTOSE-URIDINE-5'-DIPHOSPHATE;
UDP-D-GALACTOPYRANOSE
ChEMBLCHEMBL439009
DrugBankDB03501
ZINCZINC000008551104
PDB chain3hdy Chain C Residue 500 [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]
PDB3hdy Structural basis of substrate binding to UDP-galactopyranose mutase: crystal structures in the reduced and oxidized state complexed with UDP-galactopyranose and UDP.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		H109 F175 F176 Y179 T180 W184 V195 R198 Y209 F210 N296 R305 Y335 Y370
Binding residue
(residue number reindexed from 1)		H77 F143 F144 Y147 T148 W152 V163 R166 Y177 F178 N264 R273 Y303 Y338
Annotation score4
Binding affinityMOAD: Kd=66uM
Enzymatic activity
Catalytic site (original residue number in PDB) R198 R202 R275 R305 E325 Y370 N372
Catalytic site (residue number reindexed from 1) R166 R170 R243 R273 E293 Y338 N340
Enzyme Commision number 5.4.99.9: UDP-galactopyranose mutase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0008767 UDP-galactopyranose mutase activity
GO:0016853 isomerase activity
GO:0050660 flavin adenine dinucleotide binding
Cellular Component
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:3hdy, PDBe:3hdy, PDBj:3hdy
PDBsum3hdy
PubMed19836401
UniProtQ9RYF1

[Back to BioLiP]