Structure of PDB 4rqf Chain B

Receptor sequence
>4rqfB (length=474) Species: 9606 (Homo sapiens) [Search protein sequence]
VLDLDLFRVDKGGDPALIRETQEKRFKDPGLVDQLVKADSEWRRCRFRAD
NLNKLKNLCSKTIGEKMKKKEPVGDDESVPENVLSFDDLTADALANLKVS
QIKKVRLLIDEAILKCDAERIKLEAERFENLREIGNLLHPSVPISNDEDV
DNKVERIWGDCTVRKKYSHVDLVVMVDGFEGEKGAVVAGSRGYFLKGVLV
FLEQALIQYALRTLGSRGYIPIYTPFFMRKEVMQEVAQLSQFDEELYKVI
GKGSEKSDDNSYDEKYLIATSEQPIAALHRDEWLRPEDLPIKYAGLSTCF
RQEVGSHGRDTRGIFRVHQFEKIEQFVYSSPHDNKSWEMFEEMITTAEEF
YQSLGIPYHIVNIVSGSLNHAASKKLDLEAWFPGSGAFRELVSCSNCTDY
QARRLRIRYGQTKKMMDKVEFVHMLNATMCATTRTICAILENYQTKKGIT
VPEKLKEFMPPGLQELIPFVKPAP
3D structure
PDB4rqf SerRS-tRNASec complex structures reveal mechanism of the first step in selenocysteine biosynthesis.
ChainB
Resolution3.503 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) R302 R317 E391 S394 R435
Catalytic site (residue number reindexed from 1) R301 R316 E390 S393 R434
Enzyme Commision number 6.1.1.11: serine--tRNA ligase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 SER B T271 E273 N427 A428 T429 T270 E272 N426 A427 T428
BS02 ANP B R317 V318 F321 L392 A432 R435 R316 V317 F320 L391 A431 R434
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0000166 nucleotide binding
GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding
GO:0003677 DNA binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004828 serine-tRNA ligase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0019899 enzyme binding
GO:0042803 protein homodimerization activity
GO:0060090 molecular adaptor activity
GO:0098619 selenocysteine-tRNA ligase activity
Biological Process
GO:0000122 negative regulation of transcription by RNA polymerase II
GO:0001514 selenocysteine incorporation
GO:0002181 cytoplasmic translation
GO:0006400 tRNA modification
GO:0006412 translation
GO:0006418 tRNA aminoacylation for protein translation
GO:0006434 seryl-tRNA aminoacylation
GO:0016525 negative regulation of angiogenesis
GO:1904046 negative regulation of vascular endothelial growth factor production
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4rqf, PDBe:4rqf, PDBj:4rqf
PDBsum4rqf
PubMed26433229
UniProtP49591|SYSC_HUMAN Serine--tRNA ligase, cytoplasmic (Gene Name=SARS1)

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