Structure of PDB 3m4p Chain A Binding Site BS01

Receptor Information

>3m4p Chain A (length=435) Species: 5759 (Entamoeba histolytica)

TPIVCNIRDAAGLEGKLVTFKGWAYHIRKARKTLIFVELRDGSGYCQCVI
FGKELCEPEKVKLLTRECSLEITGRLNAYAGKNHPPEIADILNLEMQVTE
WKVIGESPIDLENIINKDSSIPQKMQNRHIVIRSEHTQQVLQLRSEIQWY
FRKYYHDNHFTEIQPPTIVKSTLFKLQYFNEPAYLTQSSQLYLESVIASL
GKSFCMLSSYRAEQSRTVRHLAEYLHLEAELPFISFEDLLNHLEDLVCTV
IDNVMAVHGDKIRKMNPHLKLPTRPFKRMTYADAIKYCNDHGILNKDKPF
EYGEDISEKPERQMTDEIGCPIFMIHFPSKMKAFYMSKVPGHPDLTESVD
LLMPGVGEIVGGSMRIWNYDELMGAYKANGLNPDPYYWYTQQRKYGSCPH
GGYGLGVERLVMWLLGEDHIRKVCLYPRYLERCEP

Ligand information

• Ligand ID: 4AD
• InChI: InChI=1S/C14H20N7O9P/c15-5(1-7(16)22)14(25)30-31(26,27)28-2-6-9(23)10(24)13(29-6)21-4-20-8-11(17)18-3-19-12(8)21/h3-6,9-10,13,23-24H,1-2,15H2,(H2,16,22)(H,26,27)(H2,17,18,19)/p+1/t5-,6+,9+,10+,13+/m0/s1
• InChIKey: BZHVCXQAFQWXPZ-VWJPMABRSA-O
• SMILES:
  CACTVS 3.341: NC(=O)C[CH]([NH3+])C(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
  CACTVS 3.341: NC(=O)C[C@H]([NH3+])C(=O)O[P@@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
  ACDLabs 10.04: O=C(N)CC(C(=O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O)[NH3+]
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OC(=O)C(CC(=O)N)[NH3+])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)N)[NH3+])O)O)N
• Formula: C14 H21 N7 O9 P
• Name: 4-AMINO-1,4-DIOXOBUTAN-2-AMINIUM ADENOSINE-5'-MONOPHOSPHATE;
  ASNAMP
• PDB chain: 3m4p Chain A Residue 500

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3m4p X-ray crystal structure of asparaginyl-tRNA synthetase from the eukaryotic human pathogen Entamoeba histolytica.
• Resolution: 2.83 Å
• Binding residue (original residue number in PDB): S204 Q206 R227 H236 L237 Y240 H242 E374 I375 V376 R381 Y419 G420 G422 R425
• Binding residue (residue number reindexed from 1): S188 Q190 R211 H220 L221 Y224 H226 E358 I359 V360 R365 Y403 G404 G406 R409
• Annotation score: 3

Enzymatic activity

• Catalytic site (original residue number in PDB): R227 E229 R235 H236 E374 G377 R425
• Catalytic site (residue number reindexed from 1): R211 E213 R219 H220 E358 G361 R409
• Enzyme Commision number: 6.1.1.22: asparagine--tRNA ligase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0003676 nucleic acid binding
• GO:0004812 aminoacyl-tRNA ligase activity
• GO:0004816 asparagine-tRNA ligase activity
• GO:0005524 ATP binding

Biological Process

• GO:0006412 translation
• GO:0006418 tRNA aminoacylation for protein translation
• GO:0006421 asparaginyl-tRNA aminoacylation

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:3m4p, PDBe:3m4p, PDBj:3m4p
• PDBsum: 3m4p
• UniProt: C4LWW8