Structure of PDB 1obc Chain A Binding Site BS04

Receptor Information
>1obc Chain A (length=811) Species: 262724 (Thermus thermophilus HB27) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MEKYNPHAIEAKWQRFWEEKGFMKAKDLPGKQYVLVMFPYPSGDLHMGHL
KNYTMGDVLARFRRMQGYEVLHPMGWDAFGLPAENAALKFGVHPKDWTYA
NIRQAKESLRLMGILYDWDREVTTCEPEYYRWNQWIFLKMWEKGLAYRAK
GLVNWCPKCQTVLANEQVVEGRCWRHEDTPVEKRELEQWYLRITAYAERL
LKDLEGLNWPEKVKAMQRAWIGRSEGAEILFPVEGKEVRIPVFTTRPDTL
FGATFLVLAPEHPLTLELAAPEKREEVLAYVEAAKRKTEIERQAEGREKT
GVFLGAYALNPATGERIPIWTADYVLFGYGTGAIMAVPAHDQRDYEFARK
FGLPIKKVIERPGEPLPEPLERAYEEPGIMVNSGPFDGTESEEGKRKVIA
WLEEKGLGKGRVTYRLRDWLISRQRYWGTPIPMVHCEACGVVPVPEEELP
VLLPDLKDVEDIRPKGKSPLEAHPEFYETTCPKCGGPAKRDTDTMDTFFD
SSWYYLRYTDPHNDRLPFDPEKANAWMPVDQYIGGVEHAVLHLLYSRFFT
KFLHDLGMVKVEEPFQGLFTQGMVLAWTDFGPVEVEGSVVRLPEPTRIRL
EIPESALSLEDVRKMGAELRPHEDGTLHLWKPAVMSKSKGNGVMVGPFVK
EQGADIARITILFAAPPENEMVWTEEGVQGAWRFLNRIYRRVAEDREALL
ETSGVFQAEALEGKDRELYGKLHETLKKVTEDLEALRFNTAIAALMEFLN
ALYEYRKDRPVTPVYRTAIRYYLQMLFPFAPHLAEELWHWFWPDSLFEAG
WPELDEKALEK
Ligand information
Ligand IDNVA
InChIInChI=1S/C5H11NO2/c1-2-3-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/t4-/m0/s1
InChIKeySNDPXSYFESPGGJ-BYPYZUCNSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CCC[CH](N)C(O)=O
CACTVS 3.341CCC[C@H](N)C(O)=O
OpenEye OEToolkits 1.5.0CCC[C@@H](C(=O)O)N
ACDLabs 10.04O=C(O)C(N)CCC
OpenEye OEToolkits 1.5.0CCCC(C(=O)O)N
FormulaC5 H11 N O2
NameNORVALINE
ChEMBLCHEMBL55612
DrugBankDB04185
ZINCZINC000000391821
PDB chain1obc Chain A Residue 1815 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB1obc Structural and Mechanistic Basis of Pre- and Posttransfer Editing by Leucyl-tRNA Synthetase
Resolution2.1 Å
Binding residue
(original residue number in PDB)		T247 R249 D347
Binding residue
(residue number reindexed from 1)		T244 R246 D344
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) F41 H49 H52 D80 C159 C162 F501 H541 F551 V637 K640
Catalytic site (residue number reindexed from 1) F38 H46 H49 D77 C156 C159 F498 H538 F548 V634 K637
Enzyme Commision number 6.1.1.4: leucine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0002161 aminoacyl-tRNA editing activity
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004823 leucine-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:0006429 leucyl-tRNA aminoacylation
GO:0106074 aminoacyl-tRNA metabolism involved in translational fidelity
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1obc, PDBe:1obc, PDBj:1obc
PDBsum1obc
PubMed12718881
UniProtQ72GM3

[Back to BioLiP]