Structure of PDB 1nj5 Chain A Binding Site BS03

Receptor Information
>1nj5 Chain A (length=463) Species: 187420 (Methanothermobacter thermautotrophicus str. Delta H) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EFSEWFHNILEEAEIIDQRYPVKGMHVWMPHGFMIRKNTLKILRRILDRD
HEEVLFPLLVPEDELAKEAIHVKGFEDEVYWVTHGGLSKLQRKLALRPTS
ETVMYPMFALWVRSHTDLPMRFYQVVNTFRYETKHTRPLIRVREITTFKE
AHTIHATASEAEEQVERAVEIYKEFFNSLGIPYLITRRPPWDKFPGSEYT
VAFDTLMPDGKTLQIGTVHNLGQTFARTFEIKFETPEGDHEYVHQTCYGL
SDRVIASVIAIHGDESGLCLPPDVAAHQVVIVPIIFKKAAEEVMEACREL
RSRLEAAGFRVHLDDRDIRAGRKYYEWEMRGVPLRVEIGPRDLEKGAAVI
SRRDTGEKVTADLQGIEETLRELMKDILENLRTRAWERMESEIREAETLE
EASRIVDEKRGIISFMWCGEEECGMDVEEKVRVDILGIQEEGSGTCINCG
REAPYRAYLARTY
Ligand information
Ligand IDP5A
InChIInChI=1S/C15H21N7O7S/c16-12-9-13(19-5-18-12)22(6-20-9)15-11(24)10(23)8(29-15)4-28-30(26,27)21-14(25)7-2-1-3-17-7/h5-8,10-11,15,17,23-24H,1-4H2,(H,21,25)(H2,16,18,19)/t7-,8+,10+,11+,15+/m0/s1
InChIKeyLKVJEMXWEODCAY-JVEUSOJLSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[S](=O)(=O)NC(=O)[CH]4CCCN4)[CH](O)[CH]3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[S](=O)(=O)NC(=O)[C@@H]4CCCN4)[C@@H](O)[C@H]3O
ACDLabs 10.04O=C(NS(=O)(=O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O)C4NCCC4
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COS(=O)(=O)NC(=O)[C@@H]4CCCN4)O)O)N
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COS(=O)(=O)NC(=O)C4CCCN4)O)O)N
FormulaC15 H21 N7 O7 S
Name'5'-O-(N-(L-PROLYL)-SULFAMOYL)ADENOSINE
ChEMBLCHEMBL1163086
DrugBankDB02510
ZINCZINC000013542769
PDB chain1nj5 Chain A Residue 510 [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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PDB1nj5 The structural basis of cysteine aminoacylation of tRNAPro by prolyl-tRNA synthetases
Resolution2.8 Å
Binding residue
(original residue number in PDB)		T117 E119 R148 I158 V160 I163 F166 E168 F212 Q232 T235 H237 C265 Y266 G267 S269 R271
Binding residue
(residue number reindexed from 1)		T99 E101 R130 I140 V142 I145 F148 E150 F194 Q214 T217 H219 C247 Y248 G249 S251 R253
Annotation score2
Binding affinityPDBbind-CN: -logKd/Ki=7.30,Ki=50nM
Enzymatic activity
Catalytic site (original residue number in PDB) E119 R148 H170
Catalytic site (residue number reindexed from 1) E101 R130 H152
Enzyme Commision number 6.1.1.15: proline--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004827 proline-tRNA ligase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0046872 metal ion binding
Biological Process
GO:0006412 translation
GO:0006418 tRNA aminoacylation for protein translation
GO:0006433 prolyl-tRNA aminoacylation
Cellular Component
GO:0005737 cytoplasm
GO:0017101 aminoacyl-tRNA synthetase multienzyme complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1nj5, PDBe:1nj5, PDBj:1nj5
PDBsum1nj5
PubMed12578991
UniProtO26708|SYP_METTH Proline--tRNA ligase (Gene Name=proS)

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