Structure of PDB 7nub Chain A Binding Site BS01

Receptor Information
>7nub Chain A (length=773) Species: 485 (Neisseria gonorrhoeae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MQEHYQPAAIEPAAQKKWDDARISNVSEDASKPKYYCLSMFPYPSGKLHM
GHVRNYTIGDVLSRFKLLNGFNVMQPMGWDAFGMPAENAAMKNNVAPAAW
TYDNIEYMKTQLKSLGFAVDWEREVATCKPEYYRWEQWLFTKLFEKGIVY
RKNGTVNWDPVDQTVLANEQVIDGRGWRSGALIEKREIPMYYFKITDYAE
ELLNDLDKLEHWPEQVKTMQRNWIGKSRGMTVRFAVSDDSKQGLEGDYAK
FLQVYTTRPDTLMGATYVAVAAEHPLATAAAADKPELQAFIAECKEKKGV
PTGRYVVNPLNGDKLEVWIANYVLWGYGDGAVMAVPAHDERDFEFAAKYN
LPKKQVIAVGDNAFDANRWQEWYGDKENGVLVNSGDLDGLDFQTAFDAVA
AKLQSQGAGEPKTQYRLRDWGISRQRYWGCPIPIVHCEKCGNVPVPADQL
PVVLPENVVPDGMGSPLAKMPEFYETSCPCCGGAAKRETDTMDTFIESSW
YFFRYMSPKFSDGMVSAESAKYWGAVDQYIGGIEHAIGHLLYARFFTKLM
RDEGLVNVDEPFERLLTQGMVVCETYYRWINPADVVISGTEKMSKSKNNG
VDPQELINAYGADTARLFMMFAAPPEQSLEWSDSGVEGAHRFLRRLWRTV
YEYLKQGGAVKAFAGNQDGLSKELKDLRHKLHSTTAKVSDDYGRRQQFNT
AIAAVMELLNQYDKTDTGSEQGRAVAQEVLEAAVRLLWPIVPHICETLWS
ELNGAKLWEAGWPTVDEAALVKS
Ligand information
Ligand IDUSB
InChIInChI=1S/C16H25N6O8P/c1-7(2)3-8(17)16(25)30-31(26,27)28-4-9-11(23)12(24)15(29-9)22-6-21-10-13(18)19-5-20-14(10)22/h5-9,11-12,15,23-24H,3-4,17H2,1-2H3,(H,26,27)(H2,18,19,20)/t8-,9+,11+,12+,15+/m0/s1
InChIKeyAXWPLGAOCISUCB-OPYVMVOTSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC(C)CC(C(=O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O)N
CACTVS 3.385CC(C)C[CH](N)C(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
CACTVS 3.385CC(C)C[C@H](N)C(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 2.0.7CC(C)C[C@@H](C(=O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)N
FormulaC16 H25 N6 O8 P
Name[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (2~{S})-2-azanyl-4-methyl-pentanoate
ChEMBL
DrugBank
ZINC
PDB chain7nub Chain A Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB7nub Partitioning of the initial catalytic steps of leucyl-tRNA synthetase is driven by an active site peptide-plane flip.
Resolution3.02 Å
Binding residue
(original residue number in PDB)
F41 P42 Y43 G51 H52 N55 D80 G544 E546 H547 H551 Q580 M582 V583 M635
Binding residue
(residue number reindexed from 1)
F41 P42 Y43 G51 H52 N55 D80 G532 E534 H535 H539 Q568 M570 V571 M593
Annotation score3
Enzymatic activity
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
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

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:7nub, PDBe:7nub, PDBj:7nub
PDBsum7nub
PubMed36038645
UniProtB4RNT1|SYL_NEIG2 Leucine--tRNA ligase (Gene Name=leuS)

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