Structure of PDB 6k9z Chain B Binding Site BS01

Receptor Information

>6k9z Chain B (length=301) Species: 178306 (Pyrobaculum aerophilum str. IM2)

MEIRKDPFTGEYILVSPCPFCPGAPETGRGWDVLILPNRYPVVTENPPEP
TAEDLYEVIPARGSSLVVVETPQHDVDDLSDLPLGQIKKILTAVAEAQRK
AEKEGNAAYFLFFRNKGKEIGVSLTHPFSQIYILPVVPPRVRAELQASYE
WYVKHGSCLHCRIVEKEEKRLVFQNRNWKAFVPFYAKWPHEVHIYPKRHR
SLLTELTDEEVADLAEALKITLCALKQVAGIPMPYIMVLHQAPLPRPTQY
YHLHFEIYGMYRPDGKLKHAAGAELGASLFTLDTTPEETAARIKAALQKC
L

Ligand information

• Ligand ID: UDP
• InChI: InChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
• InChIKey: XCCTYIAWTASOJW-XVFCMESISA-N
• SMILES:
  OpenEye OEToolkits 1.7.0: C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)OP(=O)(O)O)O)O
  CACTVS 3.370: O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
  CACTVS 3.370: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
  OpenEye OEToolkits 1.7.0: C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
  ACDLabs 12.01: O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O
• Formula: C9 H14 N2 O12 P2
• Name: URIDINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL130266
• DrugBank: DB03435
• ZINC: ZINC000004490939
• PDB chain: 6k9z Chain B Residue 1001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6k9z Unique active site formation in a novel galactose 1-phosphate uridylyltransferase from the hyperthermophilic archaeon Pyrobaculum aerophilum.
• Resolution: 1.78 Å
• Binding residue (original residue number in PDB): P31 N50 R51 L136 Q142 Y144
• Binding residue (residue number reindexed from 1): P19 N38 R39 L124 Q130 Y132
• Annotation score: 2

Enzymatic activity

• Catalytic site (original residue number in PDB): C30 C33 H86 N127 S135 H138 F140 Q142
• Catalytic site (residue number reindexed from 1): C18 C21 H74 N115 S123 H126 F128 Q130

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0008108 UDP-glucose:hexose-1-phosphate uridylyltransferase activity
• GO:0008270 zinc ion binding
• GO:0016779 nucleotidyltransferase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0005975 carbohydrate metabolic process
• GO:0006012 galactose metabolic process
• GO:0033499 galactose catabolic process via UDP-galactose

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:6k9z, PDBe:6k9z, PDBj:6k9z
• PDBsum: 6k9z
• PubMed: 31693208
• UniProt: Q8ZXN7