Structure of PDB 3a74 Chain D Binding Site BS01
Receptor Information
>3a74 Chain D (length=484) Species:
1422
(Geobacillus stearothermophilus) [
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ELNDQLRVRREKLKKIEELGVDPFGKRFERTHKAEELFELYGDLSKEELE
EQQIEVAVAGRIMTKRGMGKAGFAHIQDVTGQIQIYVRQDDVGEQQYELF
KISDLGDIVGVRGTMFKTKVGELSIKVSSYEFLTKALRPLPEKDIEQRYR
QRYLDLIMNPESKKTFITRSLIIQSMRRYLDSHGYLEVETPMMHAVAGGA
AARPFITHHNALDMTLYMRIAIELHLKRLIVGGLEKVYEIGRVFRNEGIS
TRHNPEFTMLELYEAYADFRDIMKLTENLIAHIATEVLGTTKIQYGEHLV
DLTPEWRRLHMVDAIKEYVGVDFWRQMSDEEARELAKEHGVEVAPHMTFG
HIVNEFFEQKVEDKLIQPTFIYGHPVEISPLAKKNPDDPRFTDRFELFIV
GREHANAFTELNDPIDQRQRFEEQLKEREQGNDEAHEMDEDFLEALEYGM
PPTGGLGIGVDRLVMLLTNSPSIRDVLLFPQMRH
Ligand information
Ligand ID
B4P
InChI
InChI=1S/C20H28N10O19P4/c21-15-9-17(25-3-23-15)29(5-27-9)19-13(33)11(31)7(45-19)1-43-50(35,36)47-52(39,40)49-53(41,42)48-51(37,38)44-2-8-12(32)14(34)20(46-8)30-6-28-10-16(22)24-4-26-18(10)30/h3-8,11-14,19-20,31-34H,1-2H2,(H,35,36)(H,37,38)(H,39,40)(H,41,42)(H2,21,23,25)(H2,22,24,26)/t7-,8-,11-,12-,13-,14-,19-,20-/m1/s1
InChIKey
YOAHKNVSNCMZGQ-XPWFQUROSA-N
SMILES
Software
SMILES
OpenEye OEToolkits 1.5.0
c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)O[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)N
CACTVS 3.341
Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P@](O)(=O)O[P@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)[C@@H](O)[C@H]3O
CACTVS 3.341
Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)[CH](O)[CH]3O
OpenEye OEToolkits 1.5.0
c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)N
Formula
C20 H28 N10 O19 P4
Name
BIS(ADENOSINE)-5'-TETRAPHOSPHATE
ChEMBL
CHEMBL339385
DrugBank
ZINC
ZINC000096014967
PDB chain
3a74 Chain D Residue 494 [
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Receptor-Ligand Complex Structure
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PDB
3a74
Crystal Structure of Lysyl-tRNA Synthetase from Bacillus stearothermophilus in Complex with Diadenosine Tetraphosphate (AP4A): Insights into AP4A Synthesis Mechanisms and Implication for Recognition of Discriminator Base of tRNA^Lys
Resolution
1.8 Å
Binding residue
(original residue number in PDB)
R253 E255 S258 R260 H261 N262 F265 M267 E366 E370 E411 H412 N414 G467 R470
Binding residue
(residue number reindexed from 1)
R245 E247 S250 R252 H253 N254 F257 M259 E358 E362 E403 H404 N406 G459 R462
Annotation score
4
Enzymatic activity
Catalytic site (original residue number in PDB)
R253 E255 R260 H261 E411 N414 R470
Catalytic site (residue number reindexed from 1)
R245 E247 R252 H253 E403 N406 R462
Enzyme Commision number
6.1.1.6
: lysine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000049
tRNA binding
GO:0000166
nucleotide binding
GO:0000287
magnesium ion binding
GO:0003676
nucleic acid binding
GO:0004812
aminoacyl-tRNA ligase activity
GO:0004824
lysine-tRNA ligase activity
GO:0005524
ATP binding
GO:0016740
transferase activity
GO:0046872
metal ion binding
Biological Process
GO:0006412
translation
GO:0006418
tRNA aminoacylation for protein translation
GO:0006430
lysyl-tRNA aminoacylation
Cellular Component
GO:0005737
cytoplasm
GO:0005829
cytosol
View graph for
Molecular Function
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Biological Process
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Cellular Component
External links
PDB
RCSB:3a74
,
PDBe:3a74
,
PDBj:3a74
PDBsum
3a74
PubMed
UniProt
Q9RHV9
|SYK_GEOSE Lysine--tRNA ligase (Gene Name=lysS)
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