Structure of PDB 3hdy Chain D Binding Site BS01

Receptor Information
>3hdy Chain D (length=361) Species: 1299 (Deinococcus radiodurans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GFDYLIVGAGFAGSVLAERLASSGQRVLIVDRRPHIGGNAYDCYDDAGVL
IHPYGPHIFHTNSKDVFEYLSRFTEWRPYQHRVLASVDGQLLPIPINLDT
VNRLYGLNLTSFQVEEFFASVAEKVEQVRTSEDVVVSKVGRDLYNKFFRG
YTRKQWGLDPSELDASVTARVPTRTNRDNRYFADTYQAMPLHGYTRMFQN
MLSSPNIKVMLNTDYREIADFIPFQHMIYTGPVDAFFDFCYGKLPYRSLE
FRHETHDTEQLLPTGTVNYPNDYAYTRVSEFKHITGQRHHQTSVVYEYPR
AEGDPYYPVPRPENAELYKKYEALADAAQDVTFVGRLATYRYYNMDQVVA
QALATFRRLQG
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 D Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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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)		F175 F176 Y179 T180 W184 V195 R198 Y209 F210 R305 Y335 Y370
Binding residue
(residue number reindexed from 1)		F147 F148 Y151 T152 W156 V167 R170 Y181 F182 R277 Y307 Y342
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) R170 R174 R247 R277 E297 Y342 N344
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

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