Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3VBB

Crystal Structure of Seryl-tRNA Synthetase from Human at 2.9 angstroms

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000049	molecular_function	tRNA binding
A	0000122	biological_process	negative regulation of transcription by RNA polymerase II
A	0000166	molecular_function	nucleotide binding
A	0000978	molecular_function	RNA polymerase II cis-regulatory region sequence-specific DNA binding
A	0001514	biological_process	selenocysteine incorporation
A	0002181	biological_process	cytoplasmic translation
A	0003677	molecular_function	DNA binding
A	0004812	molecular_function	aminoacyl-tRNA ligase activity
A	0004828	molecular_function	serine-tRNA ligase activity
A	0005515	molecular_function	protein binding
A	0005524	molecular_function	ATP binding
A	0005634	cellular_component	nucleus
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0006400	biological_process	tRNA modification
A	0006412	biological_process	translation
A	0006418	biological_process	tRNA aminoacylation for protein translation
A	0006434	biological_process	seryl-tRNA aminoacylation
A	0016525	biological_process	negative regulation of angiogenesis
A	0019899	molecular_function	enzyme binding
A	0042803	molecular_function	protein homodimerization activity
A	0060090	molecular_function	molecular adaptor activity
A	0070062	cellular_component	extracellular exosome
A	0098619	molecular_function	selenocysteine-tRNA ligase activity
A	1904046	biological_process	negative regulation of vascular endothelial growth factor production
B	0000049	molecular_function	tRNA binding
B	0000122	biological_process	negative regulation of transcription by RNA polymerase II
B	0000166	molecular_function	nucleotide binding
B	0000978	molecular_function	RNA polymerase II cis-regulatory region sequence-specific DNA binding
B	0001514	biological_process	selenocysteine incorporation
B	0002181	biological_process	cytoplasmic translation
B	0003677	molecular_function	DNA binding
B	0004812	molecular_function	aminoacyl-tRNA ligase activity
B	0004828	molecular_function	serine-tRNA ligase activity
B	0005515	molecular_function	protein binding
B	0005524	molecular_function	ATP binding
B	0005634	cellular_component	nucleus
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0006400	biological_process	tRNA modification
B	0006412	biological_process	translation
B	0006418	biological_process	tRNA aminoacylation for protein translation
B	0006434	biological_process	seryl-tRNA aminoacylation
B	0016525	biological_process	negative regulation of angiogenesis
B	0019899	molecular_function	enzyme binding
B	0042803	molecular_function	protein homodimerization activity
B	0060090	molecular_function	molecular adaptor activity
B	0070062	cellular_component	extracellular exosome
B	0098619	molecular_function	selenocysteine-tRNA ligase activity
B	1904046	biological_process	negative regulation of vascular endothelial growth factor production
C	0000049	molecular_function	tRNA binding
C	0000122	biological_process	negative regulation of transcription by RNA polymerase II
C	0000166	molecular_function	nucleotide binding
C	0000978	molecular_function	RNA polymerase II cis-regulatory region sequence-specific DNA binding
C	0001514	biological_process	selenocysteine incorporation
C	0002181	biological_process	cytoplasmic translation
C	0003677	molecular_function	DNA binding
C	0004812	molecular_function	aminoacyl-tRNA ligase activity
C	0004828	molecular_function	serine-tRNA ligase activity
C	0005515	molecular_function	protein binding
C	0005524	molecular_function	ATP binding
C	0005634	cellular_component	nucleus
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0006400	biological_process	tRNA modification
C	0006412	biological_process	translation
C	0006418	biological_process	tRNA aminoacylation for protein translation
C	0006434	biological_process	seryl-tRNA aminoacylation
C	0016525	biological_process	negative regulation of angiogenesis
C	0019899	molecular_function	enzyme binding
C	0042803	molecular_function	protein homodimerization activity
C	0060090	molecular_function	molecular adaptor activity
C	0070062	cellular_component	extracellular exosome
C	0098619	molecular_function	selenocysteine-tRNA ligase activity
C	1904046	biological_process	negative regulation of vascular endothelial growth factor production
D	0000049	molecular_function	tRNA binding
D	0000122	biological_process	negative regulation of transcription by RNA polymerase II
D	0000166	molecular_function	nucleotide binding
D	0000978	molecular_function	RNA polymerase II cis-regulatory region sequence-specific DNA binding
D	0001514	biological_process	selenocysteine incorporation
D	0002181	biological_process	cytoplasmic translation
D	0003677	molecular_function	DNA binding
D	0004812	molecular_function	aminoacyl-tRNA ligase activity
D	0004828	molecular_function	serine-tRNA ligase activity
D	0005515	molecular_function	protein binding
D	0005524	molecular_function	ATP binding
D	0005634	cellular_component	nucleus
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0006400	biological_process	tRNA modification
D	0006412	biological_process	translation
D	0006418	biological_process	tRNA aminoacylation for protein translation
D	0006434	biological_process	seryl-tRNA aminoacylation
D	0016525	biological_process	negative regulation of angiogenesis
D	0019899	molecular_function	enzyme binding
D	0042803	molecular_function	protein homodimerization activity
D	0060090	molecular_function	molecular adaptor activity
D	0070062	cellular_component	extracellular exosome
D	0098619	molecular_function	selenocysteine-tRNA ligase activity
D	1904046	biological_process	negative regulation of vascular endothelial growth factor production
E	0000049	molecular_function	tRNA binding
E	0000122	biological_process	negative regulation of transcription by RNA polymerase II
E	0000166	molecular_function	nucleotide binding
E	0000978	molecular_function	RNA polymerase II cis-regulatory region sequence-specific DNA binding
E	0001514	biological_process	selenocysteine incorporation
E	0002181	biological_process	cytoplasmic translation
E	0003677	molecular_function	DNA binding
E	0004812	molecular_function	aminoacyl-tRNA ligase activity
E	0004828	molecular_function	serine-tRNA ligase activity
E	0005515	molecular_function	protein binding
E	0005524	molecular_function	ATP binding
E	0005634	cellular_component	nucleus
E	0005737	cellular_component	cytoplasm
E	0005829	cellular_component	cytosol
E	0006400	biological_process	tRNA modification
E	0006412	biological_process	translation
E	0006418	biological_process	tRNA aminoacylation for protein translation
E	0006434	biological_process	seryl-tRNA aminoacylation
E	0016525	biological_process	negative regulation of angiogenesis
E	0019899	molecular_function	enzyme binding
E	0042803	molecular_function	protein homodimerization activity
E	0060090	molecular_function	molecular adaptor activity
E	0070062	cellular_component	extracellular exosome
E	0098619	molecular_function	selenocysteine-tRNA ligase activity
E	1904046	biological_process	negative regulation of vascular endothelial growth factor production
F	0000049	molecular_function	tRNA binding
F	0000122	biological_process	negative regulation of transcription by RNA polymerase II
F	0000166	molecular_function	nucleotide binding
F	0000978	molecular_function	RNA polymerase II cis-regulatory region sequence-specific DNA binding
F	0001514	biological_process	selenocysteine incorporation
F	0002181	biological_process	cytoplasmic translation
F	0003677	molecular_function	DNA binding
F	0004812	molecular_function	aminoacyl-tRNA ligase activity
F	0004828	molecular_function	serine-tRNA ligase activity
F	0005515	molecular_function	protein binding
F	0005524	molecular_function	ATP binding
F	0005634	cellular_component	nucleus
F	0005737	cellular_component	cytoplasm
F	0005829	cellular_component	cytosol
F	0006400	biological_process	tRNA modification
F	0006412	biological_process	translation
F	0006418	biological_process	tRNA aminoacylation for protein translation
F	0006434	biological_process	seryl-tRNA aminoacylation
F	0016525	biological_process	negative regulation of angiogenesis
F	0019899	molecular_function	enzyme binding
F	0042803	molecular_function	protein homodimerization activity
F	0060090	molecular_function	molecular adaptor activity
F	0070062	cellular_component	extracellular exosome
F	0098619	molecular_function	selenocysteine-tRNA ligase activity
F	1904046	biological_process	negative regulation of vascular endothelial growth factor production

Functional Information from PDB Data

site_id	AC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG A 601

Chain	Residue
A	ARG302
A	PHE316
A	PHE321

site_id	AC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE PO4 A 602

Chain	Residue
A	THR312
A	GLY314
A	ARG317

site_id	AC3
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MG B 601

Chain	Residue
B	GLU391

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE PO4 B 602

Chain	Residue
B	THR312
B	ARG317
B	ARG192
B	GLY309

site_id	AC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE PO4 C 601

Chain	Residue
C	THR312
C	ARG313

site_id	AC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE PO4 D 601

Chain	Residue
D	THR312
D	GLY314
D	ARG317

site_id	AC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE PO4 E 601

Chain	Residue
E	ARG313
E	ARG317

site_id	AC8
Number of Residues	2
Details	BINDING SITE FOR RESIDUE PO4 F 601

Chain	Residue
F	HIS170
F	ARG317

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	24
Details	BINDING: BINDING => ECO:0000269\|PubMed:24095058, ECO:0007744\|PDB:4L87

Chain	Residue	Details
A	THR271
C	ARG302
C	GLU325
C	ASN427
D	THR271
D	ARG302
D	GLU325
D	ASN427
E	THR271
E	ARG302
E	GLU325
A	ARG302
E	ASN427
F	THR271
F	ARG302
F	GLU325
F	ASN427
A	GLU325
A	ASN427
B	THR271
B	ARG302
B	GLU325
B	ASN427
C	THR271

site_id	SWS_FT_FI2
Number of Residues	12
Details	BINDING: BINDING => ECO:0000269\|PubMed:24095058, ECO:0000269\|PubMed:26433229, ECO:0007744\|PDB:4L87

Chain	Residue	Details
A	VAL318
E	GLU391
F	VAL318
F	GLU391
A	GLU391
B	VAL318
B	GLU391
C	VAL318
C	GLU391
D	VAL318
D	GLU391
E	VAL318

site_id	SWS_FT_FI3
Number of Residues	6
Details	SITE: Important for serine binding => ECO:0000269\|PubMed:28236339

Chain	Residue	Details
A	THR429
B	THR429
C	THR429
D	THR429
E	THR429
F	THR429

site_id	SWS_FT_FI4
Number of Residues	6
Details	MOD_RES: N-acetylmethionine => ECO:0007744\|PubMed:19413330

Chain	Residue	Details
A	MET1
B	MET1
C	MET1
D	MET1
E	MET1
F	MET1

site_id	SWS_FT_FI5
Number of Residues	6
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:17525332

Chain	Residue	Details
A	SER241
B	SER241
C	SER241
D	SER241
E	SER241
F	SER241

site_id	SWS_FT_FI6
Number of Residues	6
Details	MOD_RES: N6-acetyllysine => ECO:0007744\|PubMed:19608861

Chain	Residue	Details
A	LYS323
B	LYS323
C	LYS323
D	LYS323
E	LYS323
F	LYS323

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