Structure of PDB 1ivs Chain B Binding Site BS02

Receptor Information
>1ivs Chain B (length=862) Species: 274 (Thermus thermophilus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MDLPKAYDPKSVEPKWAEKWAKNPFVANPKSGKPPFVIFMPPPNVTGSLH
MGHALDNSLQDALIRYKRMRGFEAVWLPGTDHAGIATQVVVERLLLKEGK
TRHDLGREKFLERVWQWKEESGGTILKQLKRLGASADWSREAFTMDEKRS
RAVRYAFSRYYHEGLAYRAPRLVNWCPRCETTLSDLEVETEPTPGKLYTL
RYEVEGGGFIEIATVRPETVFADQAIAVHPEDERYRHLLGKRARIPLTEV
WIPILADPAVEKDFGTGALKVTPAHDPLDYEIGERHGLKPVSVINLEGRM
EGERVPEALRGLDRFEARRKAVELFREAGHLVKEEDYTIALATCSRCGTP
IEYAIFPQWWLRMRPLAEEVLKGLRRGDIAFVPERWKKVNMDWLENVKDW
NISRQLWWGHQIPAWYCEDCQAVNVPRPERYLEDPTSCEACGSPRLKRDE
DVFDTWFSSALWPLSTLGWPEETEDLKAFYPGDVLVTGYDILFLWVSRME
VSGYHFMGERPFKTVLLHGLVLDEKGQKMSKSKGNVIDPLEMVERYGADA
LRFALIYLATGGQDIRLDLRWLEMARNFANKLYNAARFVLLSREGFQAKE
DTPTLADRFMRSRLSRGVEEITALYEALDLAQAAREVYELVWSEFCDWYL
EAAKPALKAGNAHTLRTLEEVLAVLLKLLHPMMPFLTSELYQALTGKEEL
ALEAWPEPGGRDEEAERAFEALKQAVTAVRALKAEAGLPPAQEVRVYLEG
ETAPVEENLEVFRFLSRADLLPERPAKALVKAMPRVTARMPLEGLLDVEE
WRRRQEKRLKELLALAERSQRKLASPGFREKAPKEVVEAEEARLKENLEQ
AERIREALSQIG
Ligand information
Ligand IDVAA
InChIInChI=1S/C15H24N8O6S/c1-6(2)8(16)14(26)22-30(27,28)21-3-7-10(24)11(25)15(29-7)23-5-20-9-12(17)18-4-19-13(9)23/h4-8,10-11,15,21,24-25H,3,16H2,1-2H3,(H,22,26)(H2,17,18,19)/t7-,8+,10-,11-,15-/m1/s1
InChIKeyILBDFTSSTCBHRF-CYUGOOACSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC(C)[C@H](N)C(=O)N[S](=O)(=O)NC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
ACDLabs 10.04O=C(NS(=O)(=O)NCC3OC(n2cnc1c(ncnc12)N)C(O)C3O)C(N)C(C)C
OpenEye OEToolkits 1.5.0CC(C)[C@@H](C(=O)NS(=O)(=O)NC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)N
OpenEye OEToolkits 1.5.0CC(C)C(C(=O)NS(=O)(=O)NCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O)N
CACTVS 3.341CC(C)[CH](N)C(=O)N[S](=O)(=O)NC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
FormulaC15 H24 N8 O6 S
NameN-[VALINYL]-N'-[ADENOSYL]-DIAMINOSUFONE
ChEMBL
DrugBank
ZINCZINC000031976707
PDB chain1ivs Chain B Residue 991 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1ivs Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase
Resolution2.9 Å
Binding residue
(original residue number in PDB)		P41 P42 N44 H50 G52 H53 D56 D81 W456 S459 T487 G488 D490 I491 W495 H518 L520 V521 M529
Binding residue
(residue number reindexed from 1)		P41 P42 N44 H50 G52 H53 D56 D81 W456 S459 T487 G488 D490 I491 W495 H518 L520 V521 M529
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) C176 C179 C344 C347 W456 I491 W495 K528 K531
Catalytic site (residue number reindexed from 1) C176 C179 C344 C347 W456 I491 W495 K528 K531
Enzyme Commision number 6.1.1.9: valine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0002161 aminoacyl-tRNA editing activity
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004832 valine-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:0006438 valyl-tRNA aminoacylation
GO:0106074 aminoacyl-tRNA metabolism involved in translational fidelity
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1ivs, PDBe:1ivs, PDBj:1ivs
PDBsum1ivs
PubMed12554880
UniProtP96142|SYV_THETH Valine--tRNA ligase (Gene Name=valS)

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