Structure of PDB 7nu0 Chain A Binding Site BS01

Receptor Information
>7nu0 Chain A (length=865) 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
FLQVYTTRPDTLMGATYVAVAAEHPLATAAAADKPELQAFIAECKMEKKG
VPTGRYVVNPLNGDKLEVWIANYVLWGYGDGAVMAVPAHDERDFEFAAKY
NLPKKQVIAVGDNAFDANRWQEWYGDKENGVLVNSGDLDGLDFQTAFDAV
AAKLQSQGAGEPKTQYRLRDWGISRQRYWGCPIPIVHCEKCGNVPVPADQ
LPVVLPENVVPDGMGSPLAKMPEFYETSCPCCGGAAKRETDTMDTFIESS
WYFFRYMSPKFSDGMVSAESAKYWGAVDQYIGGIEHAIAHLLYARFFTKL
MRDEGLVNVDEPFERLLTQGMVVCETYYRENDKGGKDWINPADVELTFDD
KGRPVSAVLKADGLPVVISGTEKMSKSKNNGVDPQELINAYGADTARLFM
MFAAPPEQSLEWSDSGVEGAHRFLRRLWRTVYEYLKQGGAVKAFAGNQDG
LSKELKDLRHKLHSTTAKVSDDYGRRQQFNTAIAAVMELLNQYDKTDTGS
EQGRAVAQEVLEAAVRLLWPIVPHICETLWSELNGAKLWEAGWPTVDEAA
LVKSEIEVMVQVNGKLRGKITVAADASKADLEAAALANEGAVKFMEGKPA
KKIIVVPGRLVNIVV
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain7nu0 Chain A Residue 1002 [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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PDB7nu0 Partitioning of the initial catalytic steps of leucyl-tRNA synthetase is driven by an active site peptide-plane flip.
Resolution1.89 Å
Binding residue
(original residue number in PDB)		P42 Y43 S45 H49 G51 H52 N55 Y56 R178 G544 E546 H547 Q580 M582 V583 K634 M635 K637 S638
Binding residue
(residue number reindexed from 1)		P42 Y43 S45 H49 G51 H52 N55 Y56 R178 G533 E535 H536 Q569 M571 V572 K623 M624 K626 S627
Annotation score5
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

View graph for
Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7nu0, PDBe:7nu0, PDBj:7nu0
PDBsum7nu0
PubMed36038645
UniProtB4RNT1|SYL_NEIG2 Leucine--tRNA ligase (Gene Name=leuS)

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