Structure of PDB 3int Chain B Binding Site BS02

Receptor Information

>3int Chain B (length=374) Species: 573 (Klebsiella pneumoniae)

KSKKILIVGAGFSGAVIGRQLAEKGHQVHIIDQRDHIGGNSYDARDSETN
VMVHVYGPHIFHTDNETVWNYINKHAEMMPYVNRVKATVNGQVFSLPINL
HTINQFFSKTCSPDEARALIAEKGDEEQALRFIGKELYEAFFKGYTIKQW
GMQPSELPASILKRLPVRFNYDDNYFNHKFQGMPKCGYTQMIKSILNHEN
IKVDLQREFIVDERTHYDHVFYSGPLDAFYGYQYGRLGYRTLDFKKFIYQ
GDYQGCAVMNYCSVDVPYTRITEHKYFSPWEQHDGSVCYKEYSRACEEND
IPYYPIRQMGEMALLEKYLSLAENETNITFVGRLGTYRYLDMDVTIAEAL
KTAEVYLNSLTDNQPMPVFTVSVG

Ligand information

• Ligand ID: GDU
• InChI: InChI=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
• InChIKey: HSCJRCZFDFQWRP-ABVWGUQPSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C1=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 3.341: OC[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 3.341: OC[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 10.04: O=P(OC1OC(C(O)C(O)C1O)CO)(O)OP(=O)(O)OCC3OC(N2C=CC(=O)NC2=O)C(O)C3O
  OpenEye OEToolkits 1.5.0: C1=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
• Formula: C15 H24 N2 O17 P2
• Name: GALACTOSE-URIDINE-5'-DIPHOSPHATE;
  UDP-D-GALACTOPYRANOSE
• ChEMBL: CHEMBL439009
• DrugBank: DB03501
• ZINC: ZINC000008551104
• PDB chain: 3int Chain B Residue 392

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3int X-ray crystallography reveals a reduced substrate complex of UDP-galactopyranose mutase poised for covalent catalysis by flavin .
• Resolution: 2.51 Å
• Binding residue (original residue number in PDB): P59 I61 F152 Y155 W160 L172 R174 L175 Y185 F186 N270 R280 Y314 Y349
• Binding residue (residue number reindexed from 1): P58 I60 F142 Y145 W150 L162 R164 L165 Y175 F176 N260 R270 Y304 Y339
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): R174 R178 R250 R280 E301 Y349 D351
• Catalytic site (residue number reindexed from 1): R164 R168 R240 R270 E291 Y339 D341
• Enzyme Commision number: 5.4.99.9: UDP-galactopyranose mutase.

Gene Ontology

Molecular Function

• GO:0008767 UDP-galactopyranose mutase activity

External links

• PDB: RCSB:3int, PDBe:3int, PDBj:3int
• PDBsum: 3int
• PubMed: 19719175
• UniProt: Q48485|GLF1_KLEPN UDP-galactopyranose mutase (Gene Name=rfbD)