Structure of PDB 5dk4 Chain A

Receptor sequence
>5dk4A (length=328) Species: 1422 (Geobacillus stearothermophilus) [Search protein sequence]
GMKTIFSGIQPSGVITIGNYIGALRQFVELQHEYNCYFCIVDQHAITVWQ
DPHELRQNIRRLAALYLAVGIDPTQATLFIQSEVPAHAQAAWMLQCIVYI
GELERMTQFKEKSAGKEAVSAGLLTYPPLMAADILLYNTDIVPVGEDQKQ
HIELTRDLAERFNKRYGELFTIPEARIPKVGARIMSLVDPTKKMSKSDPN
PKAYITLLDDAKTIEKKIKSAVTDSEGTIRYDKEAKPGISNLLNIYSTLS
GQSIEELERQYEGKGYGVFKADLAQVVIETLRPIQERYHHWMESEELDRV
LDEGAEKANRVASEMVRKMEQAMGLGRR
3D structure
PDB5dk4 Selective Inhibition of Bacterial Tryptophanyl-tRNA Synthetases by Indolmycin Is Mechanism-based.
ChainA
Resolution1.9 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) K111 K192 K195
Catalytic site (residue number reindexed from 1) K112 K193 K196
Enzyme Commision number 6.1.1.2: tryptophan--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 A I8 Q9 S11 G17 N18 G21 V143 G144 D146 A181 I183 K192 M193 S194 K195 S196 I9 Q10 S12 G18 N19 G22 V144 G145 D147 A182 I184 K193 M194 S195 K196 S197
BS02 5BX A F5 S6 G7 Q9 H43 Y125 M129 D132 I133 V141 V143 Q147 F6 S7 G8 Q10 H44 Y126 M130 D133 I134 V142 V144 Q148 MOAD: Ki=2nM
PDBbind-CN: -logKd/Ki=8.70,Ki=2.0nM
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004830 tryptophan-tRNA ligase activity
GO:0005524 ATP binding
Biological Process
GO:0006412 translation
GO:0006418 tRNA aminoacylation for protein translation
GO:0006436 tryptophanyl-tRNA aminoacylation
Cellular Component
GO:0005737 cytoplasm

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Cellular Component
External links
PDB RCSB:5dk4, PDBe:5dk4, PDBj:5dk4
PDBsum5dk4
PubMed26555258
UniProtP00953|SYW_GEOSE Tryptophan--tRNA ligase (Gene Name=trpS)

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