Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4DPG

Crystal Structure of Human LysRS: P38/AIMP2 Complex I

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0003676	molecular_function	nucleic acid binding
A	0004812	molecular_function	aminoacyl-tRNA ligase activity
A	0004824	molecular_function	lysine-tRNA ligase activity
A	0005524	molecular_function	ATP binding
A	0005737	cellular_component	cytoplasm
A	0006418	biological_process	tRNA aminoacylation for protein translation
A	0006430	biological_process	lysyl-tRNA aminoacylation
B	0000166	molecular_function	nucleotide binding
B	0003676	molecular_function	nucleic acid binding
B	0004812	molecular_function	aminoacyl-tRNA ligase activity
B	0004824	molecular_function	lysine-tRNA ligase activity
B	0005524	molecular_function	ATP binding
B	0005737	cellular_component	cytoplasm
B	0006418	biological_process	tRNA aminoacylation for protein translation
B	0006430	biological_process	lysyl-tRNA aminoacylation
C	0000166	molecular_function	nucleotide binding
C	0003676	molecular_function	nucleic acid binding
C	0004812	molecular_function	aminoacyl-tRNA ligase activity
C	0004824	molecular_function	lysine-tRNA ligase activity
C	0005524	molecular_function	ATP binding
C	0005737	cellular_component	cytoplasm
C	0006418	biological_process	tRNA aminoacylation for protein translation
C	0006430	biological_process	lysyl-tRNA aminoacylation
D	0000166	molecular_function	nucleotide binding
D	0003676	molecular_function	nucleic acid binding
D	0004812	molecular_function	aminoacyl-tRNA ligase activity
D	0004824	molecular_function	lysine-tRNA ligase activity
D	0005524	molecular_function	ATP binding
D	0005737	cellular_component	cytoplasm
D	0006418	biological_process	tRNA aminoacylation for protein translation
D	0006430	biological_process	lysyl-tRNA aminoacylation
E	0000166	molecular_function	nucleotide binding
E	0003676	molecular_function	nucleic acid binding
E	0004812	molecular_function	aminoacyl-tRNA ligase activity
E	0004824	molecular_function	lysine-tRNA ligase activity
E	0005524	molecular_function	ATP binding
E	0005737	cellular_component	cytoplasm
E	0006418	biological_process	tRNA aminoacylation for protein translation
E	0006430	biological_process	lysyl-tRNA aminoacylation
F	0000166	molecular_function	nucleotide binding
F	0003676	molecular_function	nucleic acid binding
F	0004812	molecular_function	aminoacyl-tRNA ligase activity
F	0004824	molecular_function	lysine-tRNA ligase activity
F	0005524	molecular_function	ATP binding
F	0005737	cellular_component	cytoplasm
F	0006418	biological_process	tRNA aminoacylation for protein translation
F	0006430	biological_process	lysyl-tRNA aminoacylation
G	0000166	molecular_function	nucleotide binding
G	0003676	molecular_function	nucleic acid binding
G	0004812	molecular_function	aminoacyl-tRNA ligase activity
G	0004824	molecular_function	lysine-tRNA ligase activity
G	0005524	molecular_function	ATP binding
G	0005737	cellular_component	cytoplasm
G	0006418	biological_process	tRNA aminoacylation for protein translation
G	0006430	biological_process	lysyl-tRNA aminoacylation
H	0000166	molecular_function	nucleotide binding
H	0003676	molecular_function	nucleic acid binding
H	0004812	molecular_function	aminoacyl-tRNA ligase activity
H	0004824	molecular_function	lysine-tRNA ligase activity
H	0005524	molecular_function	ATP binding
H	0005737	cellular_component	cytoplasm
H	0006418	biological_process	tRNA aminoacylation for protein translation
H	0006430	biological_process	lysyl-tRNA aminoacylation
I	0017101	cellular_component	aminoacyl-tRNA synthetase multienzyme complex
J	0017101	cellular_component	aminoacyl-tRNA synthetase multienzyme complex
K	0017101	cellular_component	aminoacyl-tRNA synthetase multienzyme complex
L	0017101	cellular_component	aminoacyl-tRNA synthetase multienzyme complex

Functional Information from PDB Data

site_id	AC1
Number of Residues	11
Details	BINDING SITE FOR RESIDUE LYS A 601

Chain	Residue
A	GLY277
A	GLY546
A	TRP547
A	ALA278
A	ALA299
A	GLU301
A	GLU339
A	TYR341
A	ASN497
A	TYR499
A	GLU501

site_id	AC2
Number of Residues	10
Details	BINDING SITE FOR RESIDUE APC A 602

Chain	Residue
A	ARG323
A	THR330
A	HIS331
A	ASN332
A	PHE335
A	GLU494
A	GLY550
A	ARG553
A	ILE564
A	HOH721

site_id	AC3
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MG A 603

Chain	Residue
A	GLU487
A	GLU494

site_id	AC4
Number of Residues	11
Details	BINDING SITE FOR RESIDUE LYS B 601

Chain	Residue
B	GLY277
B	ALA278
B	ALA299
B	GLU301
B	GLU339
B	TYR341
B	ASN497
B	TYR499
B	GLU501
B	GLY546
B	HOH766

site_id	AC5
Number of Residues	10
Details	BINDING SITE FOR RESIDUE APC B 602

Chain	Residue
B	ARG323
B	THR330
B	HIS331
B	ASN332
B	PHE335
B	ASP445
B	GLU494
B	ARG553
B	ILE564
B	MG603

site_id	AC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG B 603

Chain	Residue
B	GLU487
B	GLU494
B	APC602

site_id	AC7
Number of Residues	12
Details	BINDING SITE FOR RESIDUE LYS C 601

Chain	Residue
C	GLY277
C	ALA278
C	ALA299
C	GLU301
C	GLU339
C	TYR341
C	ASN497
C	TYR499
C	GLU501
C	GLY546
C	TRP547
C	HOH725

site_id	AC8
Number of Residues	10
Details	BINDING SITE FOR RESIDUE APC C 602

Chain	Residue
C	ARG323
C	THR330
C	HIS331
C	ASN332
C	PHE335
C	GLU494
C	GLY550
C	ARG553
C	ILE564
C	HOH744

site_id	AC9
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MG C 603

Chain	Residue
C	GLU487
C	GLU494

site_id	BC1
Number of Residues	11
Details	BINDING SITE FOR RESIDUE LYS D 601

Chain	Residue
D	GLY277
D	ALA278
D	ALA299
D	GLU301
D	GLU339
D	TYR341
D	ASN497
D	TYR499
D	GLU501
D	GLY546
D	TRP547

site_id	BC2
Number of Residues	10
Details	BINDING SITE FOR RESIDUE APC D 602

Chain	Residue
D	ARG323
D	THR330
D	HIS331
D	ASN332
D	PHE335
D	ASP445
D	GLU494
D	ARG553
D	ILE564
D	MG603

site_id	BC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG D 603

Chain	Residue
D	ARG485
D	GLU487
D	GLU494
D	APC602

site_id	BC4
Number of Residues	11
Details	BINDING SITE FOR RESIDUE LYS E 601

Chain	Residue
E	GLU301
E	GLU339
E	TYR341
E	ASN497
E	TYR499
E	GLU501
E	GLY546
E	TRP547
E	GLY277
E	ALA278
E	ALA299

site_id	BC5
Number of Residues	11
Details	BINDING SITE FOR RESIDUE APC E 602

Chain	Residue
E	ARG323
E	THR330
E	HIS331
E	ASN332
E	PHE335
E	GLU494
E	GLY550
E	ARG553
E	ILE564
E	HOH718
E	HOH734

site_id	BC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MG E 603

Chain	Residue
E	GLU487
E	GLU494

site_id	BC7
Number of Residues	10
Details	BINDING SITE FOR RESIDUE LYS F 601

Chain	Residue
F	GLY277
F	ALA278
F	ALA299
F	GLU301
F	GLU339
F	TYR341
F	ASN497
F	TYR499
F	GLU501
F	GLY546

site_id	BC8
Number of Residues	11
Details	BINDING SITE FOR RESIDUE APC F 602

Chain	Residue
F	ARG323
F	THR330
F	HIS331
F	ASN332
F	PHE335
F	ASP445
F	GLU494
F	ARG553
F	ILE564
F	MG603
F	HOH713

site_id	BC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG F 603

Chain	Residue
F	GLU487
F	GLU494
F	APC602

site_id	CC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG F 604

Chain	Residue
C	HIS100
F	HIS215
F	HIS217
K	PRO2

site_id	CC2
Number of Residues	12
Details	BINDING SITE FOR RESIDUE LYS G 601

Chain	Residue
G	GLY277
G	ALA278
G	ALA299
G	GLU301
G	GLU339
G	TYR341
G	ASN497
G	TYR499
G	GLU501
G	GLY546
G	TRP547
G	HOH738

site_id	CC3
Number of Residues	11
Details	BINDING SITE FOR RESIDUE APC G 602

Chain	Residue
G	ARG323
G	THR330
G	HIS331
G	ASN332
G	PHE335
G	GLU494
G	GLY550
G	ARG553
G	ILE564
G	MG603
G	HOH739

site_id	CC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG G 603

Chain	Residue
G	GLU487
G	GLU494
G	APC602

site_id	CC5
Number of Residues	1
Details	BINDING SITE FOR RESIDUE ALA H 601

Chain	Residue
H	PRO575

site_id	CC6
Number of Residues	10
Details	BINDING SITE FOR RESIDUE LYS H 602

Chain	Residue
H	GLY277
H	ALA278
H	ALA299
H	GLU301
H	GLU339
H	TYR341
H	ASN497
H	TYR499
H	GLU501
H	GLY546

site_id	CC7
Number of Residues	11
Details	BINDING SITE FOR RESIDUE APC H 603

Chain	Residue
H	ARG323
H	THR330
H	HIS331
H	ASN332
H	PHE335
H	ASP445
H	GLU494
H	ARG553
H	ILE564
H	MG604
H	HOH707

site_id	CC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG H 604

Chain	Residue
H	GLU487
H	GLU494
H	APC603

site_id	CC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG H 605

Chain	Residue
A	HIS100
H	HIS215
H	HIS217
I	PRO2

site_id	DC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG J 101

Chain	Residue
B	HIS215
B	HIS217
G	HIS100
J	PRO2

site_id	DC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG L 101

Chain	Residue
D	HIS215
D	HIS217
E	HIS100
L	PRO2

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	BINDING: BINDING => ECO:0000269\|PubMed:18272479, ECO:0000269\|PubMed:26074468

Chain	Residue	Details
A	GLY277
B	GLY277
C	GLY277
D	GLY277
E	GLY277
F	GLY277
G	GLY277
H	GLY277

site_id	SWS_FT_FI2
Number of Residues	40
Details	BINDING: BINDING => ECO:0000269\|PubMed:18272479, ECO:0000269\|PubMed:23159739, ECO:0000269\|PubMed:26074468

Chain	Residue	Details
A	GLU301
B	GLU501
C	GLU301
C	GLU339
C	TYR341
C	ASN497
C	GLU501
D	GLU301
D	GLU339
D	TYR341
D	ASN497
A	GLU339
D	GLU501
E	GLU301
E	GLU339
E	TYR341
E	ASN497
E	GLU501
F	GLU301
F	GLU339
F	TYR341
F	ASN497
A	TYR341
F	GLU501
G	GLU301
G	GLU339
G	TYR341
G	ASN497
G	GLU501
H	GLU301
H	GLU339
H	TYR341
H	ASN497
A	ASN497
H	GLU501
A	GLU501
B	GLU301
B	GLU339
B	TYR341
B	ASN497

site_id	SWS_FT_FI3
Number of Residues	32
Details	BINDING: BINDING => ECO:0000269\|PubMed:18272479

Chain	Residue	Details
A	ARG323
C	HIS331
C	GLU494
C	GLY550
D	ARG323
D	HIS331
D	GLU494
D	GLY550
E	ARG323
E	HIS331
E	GLU494
A	HIS331
E	GLY550
F	ARG323
F	HIS331
F	GLU494
F	GLY550
G	ARG323
G	HIS331
G	GLU494
G	GLY550
H	ARG323
A	GLU494
H	HIS331
H	GLU494
H	GLY550
A	GLY550
B	ARG323
B	HIS331
B	GLU494
B	GLY550
C	ARG323

site_id	SWS_FT_FI4
Number of Residues	16
Details	MOD_RES: N6-acetyllysine => ECO:0007744\|PubMed:19608861

Chain	Residue	Details
A	LYS88
E	LYS141
F	LYS88
F	LYS141
G	LYS88
G	LYS141
H	LYS88
H	LYS141
A	LYS141
B	LYS88
B	LYS141
C	LYS88
C	LYS141
D	LYS88
D	LYS141
E	LYS88

site_id	SWS_FT_FI5
Number of Residues	8
Details	MOD_RES: Phosphoserine => ECO:0000269\|PubMed:19524539

Chain	Residue	Details
A	SER207
B	SER207
C	SER207
D	SER207
E	SER207
F	SER207
G	SER207
H	SER207

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)