Structure of PDB 1yfr Chain B Binding Site BS03

Receptor Information
>1yfr Chain B (length=448) Species: 63363 (Aquifex aeolicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLSAHEIRELFLSFFEKKGHTRVKSAPLVPENDPTLLFVNAGMVPFKNVF
LGLEKRPYKRATSCQKCLRVSGKHNDLEQVGYTSRHHTFFEMLGNFSFGD
YFKKEAIEYAWEFVTEVLKLPKEKLYVSVYKDDEEAYRIWNEHIGIPSER
IWRLGEEDNFWQMGDVGPCGPSSEIYVDRGEEYEGDERYLEIWNLVFMQY
NRDENGVLTPLPHPNIDTGMGLERIASVLQGKNSNFEIDIIFPLIQFGEE
VSGKKYGEKFETDVALRVIADHLRAITFAISDGVIPSNEGRGYVIRRILR
RAMRFGYKLGIENPFLYKGVDLVVDIMKEPYPELELSREFVKGIVKGEEK
RFIKTLKAGMEYIQEVIQKALEEGRKTLSGKEVFTAYDTYGFPVDLIDEI
AREKGLGIDLEGFQCELEEQRERARKHPVYSHLKELGKTSAFVGAAAL
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain1yfr Chain B Residue 2500 [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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PDB1yfr Breaking sieve for steric exclusion of a noncognate amino acid from active site of a tRNA synthetase.
Resolution2.15 Å
Binding residue
(original residue number in PDB)		R69 R85 H86 H87 F90 M92 E191 G221 R224
Binding residue
(residue number reindexed from 1)		R69 R85 H86 H87 F90 M92 E191 G221 R224
Annotation score5
Enzymatic activity
Enzyme Commision number 6.1.1.7: alanine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003676 nucleic acid binding
GO:0004813 alanine-tRNA ligase activity
GO:0005524 ATP binding
Biological Process
GO:0006419 alanyl-tRNA aminoacylation
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1yfr, PDBe:1yfr, PDBj:1yfr
PDBsum1yfr
PubMed15657145
UniProtO67323|SYA_AQUAE Alanine--tRNA ligase (Gene Name=alaS)

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