Structure of PDB 3q4d Chain E Binding Site BS03

Receptor Information

>3q4d Chain E (length=368) Species: 269798 (Cytophaga hutchinsonii ATCC 33406)

MIITQVELYKSPVKLKEPFKISLGILTHANNVIVRIHTASGHIGYGECSP
FMTIHGESMDTAFIVGQYLAKGLIGTSCLDIVSNSLLMDAIIYGNSCIKS
AFNIALYDLAAQHAGLPLYAFLGGKKDKIIQTDYTVSIDEPHKMAADAVQ
IKKNGFEIIKVKVGGSKELDVERIRMIREAAGDSITLRIDANQGWSVETA
IETLTLLEPYNIQHCEEPVSRNLYTALPKIRQACRIPIMADESCCNSFDA
ERLIQIQACDSFNLKLSKSAGITNALNIIRLAEQAHMPVQVGGFLESRLG
FTAAAHVALVSKTICYYDFDTPLMFEADPVRGGIVYQQRGIIEVPETAGL
GAGYQKDYLSGLEKICIN

Ligand information

• Ligand ID: ALA
• InChI: InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m0/s1
• InChIKey: QNAYBMKLOCPYGJ-REOHCLBHSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC(C(=O)O)N
  CACTVS 3.341: C[CH](N)C(O)=O
  ACDLabs 10.04: O=C(O)C(N)C
  CACTVS 3.341: C[C@H](N)C(O)=O
  OpenEye OEToolkits 1.5.0: C[C@@H](C(=O)O)N
• Formula: C3 H7 N O2
• Name: ALANINE
• ChEMBL: CHEMBL279597
• DrugBank: DB00160
• ZINC: ZINC000004658553
• PDB chain: 3q4d Chain E Residue 2479

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3q4d Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): K162 D190 D241 K265 G293
• Binding residue (residue number reindexed from 1): K162 D190 D241 K265 G293
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): F19 P50 T53 T135 K160 K162 D190 N192 E216 D241 E242 S243 K265 G292 G293 F294 Y317 D318 F319
• Catalytic site (residue number reindexed from 1): F19 P50 T53 T135 K160 K162 D190 N192 E216 D241 E242 S243 K265 G292 G293 F294 Y317 D318 F319
• Enzyme Commision number: 5.1.1.-

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0016853 isomerase activity
• GO:0016854 racemase and epimerase activity
• GO:0016855 racemase and epimerase activity, acting on amino acids and derivatives
• GO:0046872 metal ion binding

Biological Process

• GO:0006518 peptide metabolic process

External links

• PDB: RCSB:3q4d, PDBe:3q4d, PDBj:3q4d
• PDBsum: 3q4d
• PubMed: 22392983
• UniProt: Q11T61|AAEP_CYTH3 D-Ala-D/L-Ala epimerase (Gene Name=tfdD)