Structure of PDB 3nem Chain B

Receptor sequence
>3nemB (length=438) Species: 311400 (Thermococcus kodakarensis) [Search protein sequence]
MYRTHYSSEITEELNGQKVKVAGWVWEVKDLGGIKFLWIRDRDGIVQITA
PKKKVDPELFKLIPKLRSEDVVAVEGVVNFTPKAKLGFEILPEKIVVLNR
AETPLPLDPTGKVKAELDTRLDNRFMDLRRPEVMAIFKIRSSVFKAVRDF
FHENGFIEIHTPKIIATATEGGTELFPMKYFEEDAFLAQSPQLYKQIMMA
SGLDRVYEIAPIFRAEEHNTTRHLNEAWSIDSEMAFIEDEEEVMSFLERL
VAHAINYVREHNAKELDILNFELEEPKLPFPRVSYDKALEILGDLGKEIP
WGEDIDTEGERLLGKYMMENENAPLYFLYQYPSEAKPFYIMKYDNKPEIC
RAFDLEYRGVEISSGGQREHRHDILVEQIKEKGLNPESFEFYLKAFRYGM
PPHGGFGLGAERLIKQMLDLPNIREVILFPRDRRRLTP
3D structure
PDB3nem Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation
ChainB
Resolution1.89 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) R214 E216 R222 H223 E361 S364 R412
Catalytic site (residue number reindexed from 1) R214 E216 R222 H223 E361 S364 R412
Enzyme Commision number 6.1.1.12: aspartate--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 ATP B R214 E216 H223 L224 E361 I362 S363 S364 G407 G409 R412 R214 E216 H223 L224 E361 I362 S363 S364 G407 G409 R412
BS02 MG B E361 S364 E361 S364
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0000287 magnesium ion binding
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004815 aspartate-tRNA ligase activity
GO:0005524 ATP binding
GO:0046872 metal ion binding
Biological Process
GO:0006412 translation
GO:0006418 tRNA aminoacylation for protein translation
GO:0006422 aspartyl-tRNA aminoacylation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0017101 aminoacyl-tRNA synthetase multienzyme complex

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Cellular Component
External links
PDB RCSB:3nem, PDBe:3nem, PDBj:3nem
PDBsum3nem
PubMed9724658
UniProtQ52428|SYD_THEKO Aspartate--tRNA(Asp) ligase (Gene Name=aspS)

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