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Structure of PDB 1il2 Chain A Binding Site BS02

Receptor Information

>1il2 Chain A (length=585) Species: 562 (Escherichia coli)

MRTEYCGQLRLSHVGQQVTLCGWVNRRRDLGSLIFIDMRDREGIVQVFFD
PDRADALKLASELRNEFCIQVTGTVRARDEKNINRDMATGEIEVLASSLT
IINRADVLPLDSNHVNTEEARLKYRYLDLRRPEMAQRLKTRAKITSLVRR
FMDDHGFLDIETPMLTKATPEGARDYLVPSRVHKGKFYALPQSPQLFKQL
LMMSGFDRYYQIVKCFRDEDLRADRQPEFTQIDVETSFMTAPQVREVMEA
LVRHLWLEVKGVDLGDFPVMTFAEAERRYGSDKPDLRNPMELTDVADLLK
SVEFAVFAGPANDPKGRVAALRVPGGASLTRKQIDEYGNFVKIYGAKGLA
YIKVNERAKGLEGINSPVAKFLNAEIIEDILDRTAAQDGDMIFFGADNKK
IVADAMGALRLKVGKDLGLTDESKWAPLWVIDFPMFEDDGEGGLTAMHHP
FTSPKDMTAAELKAAPENAVANAYDMVINGYEVGGGSVRIHNGDMQQTVF
GILGINEEEQREKFGFLLDALKYGTPPHAGLAFGLDRLTMLLTGTDNIRD
VIAFPKTTAAACLMTEAPSFANPTALAELSIQVVK

Ligand information

• Ligand ID: AMO
• InChI: InChI=1S/C14H19N6O10P/c15-5(1-7(21)22)14(25)30-31(26,27)28-2-6-9(23)10(24)13(29-6)20-4-19-8-11(16)17-3-18-12(8)20/h3-6,9-10,13,23-24H,1-2,15H2,(H,21,22)(H,26,27)(H2,16,17,18)/t5-,6+,9+,10+,13+/m0/s1
• InChIKey: QPBSGQWTJLPZNF-VWJPMABRSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OC(=O)C(CC(=O)O)N)O)O)N
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OC(=O)[C@H](CC(=O)O)N)O)O)N
  CACTVS 3.341: N[CH](CC(O)=O)C(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
  ACDLabs 10.04: O=C(O)CC(N)C(=O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  CACTVS 3.341: N[C@@H](CC(O)=O)C(=O)O[P@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
• Formula: C14 H19 N6 O10 P
• Name: ASPARTYL-ADENOSINE-5'-MONOPHOSPHATE
• DrugBank: DB01895
• ZINC: ZINC000031976613
• PDB chain: 1il2 Chain A Residue 831

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1il2 The structure of an AspRS-tRNA(Asp) complex reveals a tRNA-dependent control mechanism.
• Resolution: 2.6 Å
• Binding residue (original residue number in PDB): E171 S193 Q195 K198 R217 Q226 F229 Q231 H448 E482 V483 G484 G485 R489 L531 A532 G534 R537
• Binding residue (residue number reindexed from 1): E171 S193 Q195 K198 R217 Q226 F229 Q231 H448 E482 V483 G484 G485 R489 L531 A532 G534 R537
• Annotation score: 3

Enzymatic activity

• Catalytic site (original residue number in PDB): E482 G485 R537
• Catalytic site (residue number reindexed from 1): E482 G485 R537
• Enzyme Commision number: 6.1.1.12: aspartate--tRNA ligase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0003676 nucleic acid binding
• GO:0004812 aminoacyl-tRNA ligase activity
• GO:0004815 aspartate-tRNA ligase activity
• GO:0005524 ATP binding
• GO:0016874 ligase activity

Biological Process

• GO:0006412 translation
• GO:0006418 tRNA aminoacylation for protein translation
• GO:0006422 aspartyl-tRNA aminoacylation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:1il2, PDBe:1il2, PDBj:1il2
• PDBsum: 1il2
• PubMed: 11566892
• UniProt: P21889|SYD_ECOLI Aspartate--tRNA ligase (Gene Name=aspS)

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