Structure of PDB 6vtf Chain D Binding Site BS01

Receptor Information
>6vtf Chain D (length=337) Species: 5762 (Naegleria gruberi) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VRKLATIRTAGEITPIAGAEAIECCHVDGWTCVIKKGEFKQGDRGVYFEI
DSFIKEDNDRYPMLSKQVIDYEGQRGTRLRTARLRGQLSQGLFLPMDRFP
ELASNQVGDDVTEILGITKWEPPISTNLSGEILGEFPTFISKTDQERVQN
LIPQIEENKGQKFEVTVKLDGSSMTVYRKDDHIGVCGRNWELRETATNAQ
WHAARRNKMIEGLQFLNRNLALQGEIIGESIQGNLEKLKGQDFYLFDIYD
IDKAQYLTPIERQSLVKQLNDNGFTVKHVPILDDLELNHTAEQILAMADG
PSLNKNVKREGLVFKRLDGKFSFKAISNAYLEKHKDR
Ligand information
Ligand IDPOP
InChIInChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)/p-2
InChIKeyXPPKVPWEQAFLFU-UHFFFAOYSA-L
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0O[P@@](=O)([O-])O[P@@](=O)(O)[O-]
CACTVS 3.341O[P]([O-])(=O)O[P](O)([O-])=O
ACDLabs 10.04[O-]P(=O)(O)OP([O-])(=O)O
OpenEye OEToolkits 1.5.0OP(=O)([O-])OP(=O)(O)[O-]
FormulaH2 O7 P2
NamePYROPHOSPHATE 2-
ChEMBL
DrugBank
ZINC
PDB chain6vtf Chain D Residue 400 [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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PDB6vtf Caveat mutator: alanine substitutions for conserved amino acids in RNA ligase elicit unexpected rearrangements of the active site for lysine adenylylation.
Resolution2.71 Å
Binding residue
(original residue number in PDB)		R4 K121 R190 K326
Binding residue
(residue number reindexed from 1)		R2 K119 R188 K324
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0046872 metal ion binding

View graph for
Molecular Function
External links
PDB RCSB:6vtf, PDBe:6vtf, PDBj:6vtf
PDBsum6vtf
PubMed32315072
UniProtD2W2Z5

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