Structure of PDB 6vt1 Chain B Binding Site BS01

Receptor Information
>6vt1 Chain B (length=339) Species: 5762 (Naegleria gruberi) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MGVRKLATIRTAGEITPIAGAEAIECCHVDGWTCVIKKGEFKQGDRGVYF
EIDSFIKEDNDRYPMLSKQVIDYEGQRGTRLRTARLRGQLSQGLFLPMDR
FPELASNQVGDDVTEILGITKWEPPISTNLSGEILGEFPTFISKTDQERV
QNLIPQIEENKGQKFEVTVKLAGSSMTVYRKDDHIGVCGRNWELRETATN
AQWHAARRNKMIEGLQFLNRNLALQGEIIGESIQGNLEKLKGQDFYLFDI
YDIDKAQYLTPIERQSLVKQLNDNGFTVKHVPILDDLELNHTAEQILAMA
DGPSLNKNVKREGLVFKRLDGKFSFKAISNAYLEKHKDR
Ligand information
Ligand IDAMP
InChIInChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyUDMBCSSLTHHNCD-KQYNXXCUSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N
ACDLabs 12.01O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
FormulaC10 H14 N5 O7 P
NameADENOSINE MONOPHOSPHATE
ChEMBLCHEMBL752
DrugBankDB00131
ZINCZINC000003860156
PDB chain6vt1 Chain B Residue 401 [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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PDB6vt1 Caveat mutator: alanine substitutions for conserved amino acids in RNA ligase elicit unexpected rearrangements of the active site for lysine adenylylation.
Resolution2.381 Å
Binding residue
(original residue number in PDB)		T145 T168 K170 L171 S175 E227 F248 V315 K317 K326
Binding residue
(residue number reindexed from 1)		T145 T168 K170 L171 S175 E227 F248 V315 K317 K326
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:6vt1, PDBe:6vt1, PDBj:6vt1
PDBsum6vt1
PubMed32315072
UniProtD2W2Z5

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