Structure of PDB 6vr8 Chain I Binding Site BS01

Receptor Information
>6vr8 Chain I (length=482) Species: 2180 (Methanothermus fervidus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ATPAGSHMRLSELASYVSGKLIGEDKEIKVGIFNTLGDANPNDIVIRHWI
DEKGVEIAKNKEVSALITQNPKGNSLEYAKKLKVPIILVNKIELASAFAI
KWTIKNFAPNTYRVVITGTNGKSTTTHMIYHILTHAGKKAFTNTDAKSEF
NTLIDPMVAKLLAEKAKKENLEYLVIEVSEVQGWLDRLMKDHAYLMTKSI
NPNVVVVTNVALDHIGLVNSIEEVFEETSGAVKALEKGFAVLNYDNEFTR
KMAKLTNKNVKVFFYGKNCPVTFKSGGIYVNNDLFIKKEELPFKSEYFIQ
NTLAAISACLCLNIPPDIIKKGILTYKPLKRRFSILCKKPLIIDDFAHNP
DGIKMAIKSAKKLTKNKLWVVCAIRGSRGKIINKLNAESLSKTLKNIENY
EVVITNSDDVVDNLNKVKKEEEKTFLKTLEKYNINYRFHKKLKTALEETL
TNCKKDDTILLIGAQGMDPASKLLKKIKVIPC
Ligand information
Ligand IDUDP
InChIInChI=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
InChIKeyXCCTYIAWTASOJW-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0C1=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 3.370O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
CACTVS 3.370O[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 1.7.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O
FormulaC9 H14 N2 O12 P2
NameURIDINE-5'-DIPHOSPHATE
ChEMBLCHEMBL130266
DrugBankDB03435
ZINCZINC000004490939
PDB chain6vr8 Chain I Residue 508 [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]
PDB6vr8 Structural characterisation of methanogen pseudomurein cell wall peptide ligases homologous to bacterial MurE/F murein peptide ligases.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		Q62 K84 E86 W177 R180 L181 K183
Binding residue
(residue number reindexed from 1)		Q69 K91 E93 W184 R187 L188 K190
Annotation score4
Enzymatic activity
Enzyme Commision number 6.3.2.-
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0005524 ATP binding
GO:0016874 ligase activity
GO:0016881 acid-amino acid ligase activity
Biological Process
GO:0009058 biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6vr8, PDBe:6vr8, PDBj:6vr8
PDBsum6vr8
PubMed36178458
UniProtE3GZ29

[Back to BioLiP]