Structure of PDB 6ild Chain B Binding Site BS03

Receptor Information
>6ild Chain B (length=499) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DPNQYYKIRSQAIHQLKVNGEDPYPHKFHVDISLTDFIQKYSHLQPGDHL
TDITLKVAGRIHAKRASGGKLIFYDLRGEGVKLQVMANSRNYKSEEEFIH
INNKLRRGDIIGVQGNPGKTKKGELSIIPYEITLLSPCLHMLPHLDKETR
YRQRYLDLILNDFVRQKFIIRSKIITYIRSFLDELGFLEIETPMMNIIPG
GAVAKPFITYHNELDMNLYMRIAPELYHKMLVVGGIDRVYEIGRQFRNEG
IDLTHNPEFTTCEFYMAYADYHDLMEITEKMVSGMVKHITGSYKVTYHPD
GPEGQAYDVDFTPPFRRINMVEELEKALGMKLPETNLFETEETRKILDDI
CVAKAVECPPPRTTARLLDKLVGEFLEVTCINPTFICDHPQIMSPLAKWH
RSKEGLTERFELFVMKKEICNAYTELNDPMRQRQLFEEQAKAKAAGDDEA
MFIDENFCTALEYGLPPTAGWGMGIDRVAMFLTDSNNIKEVLLFPAMKP
Ligand information
Ligand ID45A
InChIInChI=1S/C11H16N5O6P/c1-23(19,20)21-2-5-7(17)8(18)11(22-5)16-4-15-6-9(12)13-3-14-10(6)16/h3-5,7-8,11,17-18H,2H2,1H3,(H,19,20)(H2,12,13,14)/t5-,7-,8-,11-/m1/s1
InChIKeyPXSSQXBLDTZHLF-IOSLPCCCSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=P(O)(OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O)C
OpenEye OEToolkits 1.9.2CP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
CACTVS 3.385C[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
CACTVS 3.385C[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.9.2CP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
FormulaC11 H16 N5 O6 P
Name5'-O-[(S)-hydroxy(methyl)phosphoryl]adenosine
ChEMBL
DrugBankDB02798
ZINCZINC000003914599
PDB chain6ild Chain B Residue 605 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6ild Retractile lysyl-tRNA synthetase-AIMP2 assembly in the human multi-aminoacyl-tRNA synthetase complex.
Resolution1.882 Å
Binding residue
(original residue number in PDB)		T330 H331 F335 E494 R553
Binding residue
(residue number reindexed from 1)		T254 H255 F259 E418 R477
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) R323 E325 T330 H331 E494 N497 R553
Catalytic site (residue number reindexed from 1) R247 E249 T254 H255 E418 N421 R477
Enzyme Commision number 2.7.7.-
6.1.1.6: lysine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003676 nucleic acid binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004824 lysine-tRNA ligase activity
GO:0005524 ATP binding
Biological Process
GO:0006418 tRNA aminoacylation for protein translation
GO:0006430 lysyl-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:6ild, PDBe:6ild, PDBj:6ild
PDBsum6ild
PubMed30733335
UniProtQ15046|SYK_HUMAN Lysine--tRNA ligase (Gene Name=KARS1)

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