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BioLiP

Structure of PDB 4kr3 Chain A Binding Site BS03

Receptor Information

>4kr3 Chain A (length=466) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

VDRAKMGDTLKRRFFYDQAFAIYGGVSGLYDFGPVGCALKNNIIQTWRQH
FIQEEQILEIDCTMLTPEPVLKTSGHVDKFSFNLMFKTFIGPGGNMPGYL
RPETAQGIFLNFKRLLEFNQGKLPFAAAQIGNSFRNEISPRSGLIRVREF
TMAEIEHFVDPSEKDHPKFQNVADLHLYLYSAKAQVSGQSARKMRLGDAV
EQGVINNTVLGYFIGRIYLYLTKVGISPDKLRFRQHMENACDCWDAESKT
SYGWIEIVGCADRSCYDLSCHARATKVPLVAEKPLKEPKTVNVVFQKTLY
VEEVVPNVIEPSFGLGRIMYTVFEHTFHVREGDEQRTFFSFPAVVAPFKC
SVLPLSQNQEFMPFVKELSEALTRHGVSHKVDDSSGSIGRRYARTDEIGV
AFGVTIDFDTVNKTPHTATLRDRDSMRQIRAEISELPSIVQDLANGNITW
ADVEARYPLFEGQETG

Ligand information

Ligand ID

ANP

InChI

InChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1

InChIKey

PVKSNHVPLWYQGJ-KQYNXXCUSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.7.0	c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
CACTVS 3.370	Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370	Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
ACDLabs 12.01	O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.0	c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N

Formula

C10 H17 N6 O12 P3

Name

PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

PDB chain

4kr3 Chain A Residue 702 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	4kr3 Cocrystal Structures of Glycyl-tRNA Synthetase in Complex with tRNA Suggest Multiple Conformational States in Glycylation
Resolution	3.235 Å
Binding residue (original residue number in PDB)	R277 I287 R288 V289 F292 H378 E403 I404
Binding residue (residue number reindexed from 1)	R135 I145 R146 V147 F150 H236 E256 I257
Annotation score	3

Enzymatic activity

Enzyme Commision number

2.7.7.-
6.1.1.14: glycine--tRNA ligase.

Gene Ontology

	Molecular Function
GO:0000166	nucleotide binding
GO:0004812	aminoacyl-tRNA ligase activity
GO:0004820	glycine-tRNA ligase activity
GO:0005524	ATP binding

	Biological Process
GO:0006418	tRNA aminoacylation for protein translation
GO:0006426	glycyl-tRNA aminoacylation

	Cellular Component
GO:0005737	cytoplasm

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Cellular Component

External links

PDB	RCSB:4kr3, PDBe:4kr3, PDBj:4kr3
PDBsum	4kr3
PubMed	24898252
UniProt	P41250\|GARS_HUMAN Glycine--tRNA ligase (Gene Name=GARS1)

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