Structure of PDB 1ygb Chain A Binding Site BS01

Receptor Information

>1ygb Chain A (length=448) Species: 63363 (Aquifex aeolicus)

SLSAHEIRELFLSFFEKKGHTRVKSAPLVPENDPTLLFVNAGMVPFKNVF
LGLEKRPYKRATSCQKCLRVSGKHNDLEQVGYTSRHHTFFEMLGNFSFGD
YFKKEAIEYAWEFVTEVLKLPKEKLYVSVYKDDEEAYRIWNEHIGIPSER
IWRLGEEDNFWQMGDVGPCGPSSEIYVDRGEEYEGDERYLEIWNLVFMQY
NRDENGVLTPLPHPNIDTGMGLERIASVLQGKNSNFEIDIIFPLIQFGEE
VSGKKYGEKFETDVALRVIADHLRAITFAISDGVIPSNEGRGYVIRRILR
RAMRFGYKLGIENPFLYKGVDLVVDIMKEPYPELELSREFVKGIVKGEEK
RFIKTLKAGMEYIQEVIQKALEEGRKTLSGKEVFTAYDTYGFPVDLIDEI
AREKGLGIDLEGFQCELEEQRERARKHPVYSHLKELGKTSAFVGAAAL

Ligand information

• Ligand ID: SER
• InChI: InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/t2-/m0/s1
• InChIKey: MTCFGRXMJLQNBG-REOHCLBHSA-N
• SMILES:
  CACTVS 3.341: N[CH](CO)C(O)=O
  OpenEye OEToolkits 1.5.0: C(C(C(=O)O)N)O
  CACTVS 3.341: N[C@@H](CO)C(O)=O
  ACDLabs 10.04: O=C(O)C(N)CO
  OpenEye OEToolkits 1.5.0: C([C@@H](C(=O)O)N)O
• Formula: C3 H7 N O3
• Name: SERINE
• ChEMBL: CHEMBL11298
• DrugBank: DB00133
• ZINC: ZINC000000895034
• PDB chain: 1ygb Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1ygb Breaking sieve for steric exclusion of a noncognate amino acid from active site of a tRNA synthetase.
• Resolution: 2.48 Å
• Binding residue (original residue number in PDB): M92 N194 D217 T218 G219
• Binding residue (residue number reindexed from 1): M92 N194 D217 T218 G219
• Annotation score: 2

Enzymatic activity

• Enzyme Commision number: 6.1.1.7: alanine--tRNA ligase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0003676 nucleic acid binding
• GO:0004813 alanine-tRNA ligase activity
• GO:0005524 ATP binding

Biological Process

• GO:0006419 alanyl-tRNA aminoacylation

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:1ygb, PDBe:1ygb, PDBj:1ygb
• PDBsum: 1ygb
• PubMed: 15657145
• UniProt: O67323|SYA_AQUAE Alanine--tRNA ligase (Gene Name=alaS)