Structure of PDB 4dn1 Chain A Binding Site BS01

Receptor Information

>4dn1 Chain A (length=389) Species: 176299 (Agrobacterium fabrum str. C58)

HMNSPIATVEVFTLTQPRKVPYLGALREGEVVNPNGYIVRKGNRTVYPTF
DRSVLVRMTTEAGTVGWGETYGIVAPGAVAALINDLLAGFVIGRDASDPS
AVYDDLYDMMRVRGYTGGFYVDALAALDIALWDIAGQEAGKSIRDLLGGG
VDSFPAYVSGLPERTLKARGELAKYWQDRGFNAFKFATPVADDGPAAEIA
NLRQVLGPQAKIAADMHWNQTPERALELIAEMQPFDPWFAEAPVWTEDIA
GLEKVSKNTDVPIAVGEEWRTHWDMRARIERCRIAIVQPEMGHKGITNFI
RIGALAAEHGIDVIPHATVGAGIFLAASLQASSTLSMLKGHEFQHSIFEP
NRRLLDGDMDCREGRYHLPSGPGLGVRPSEAALGLIERI

Ligand information

• Ligand ID: MG
• InChI: InChI=1S/Mg/q+2
• InChIKey: JLVVSXFLKOJNIY-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mg+2]
  CACTVS 3.341: [Mg++]
• Formula: Mg
• Name: MAGNESIUM ION
• DrugBank: DB01378
• PDB chain: 4dn1 Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4dn1 Crystal structure of an enolase (mandelate racemase subgroup member) from Agrobacterium tumefaciens (target EFI-502088) with bound mg and formate
• Resolution: 2.05 Å
• Binding residue (original residue number in PDB): D214 E240 E266
• Binding residue (residue number reindexed from 1): D215 E241 E267
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): F180 A182 K184 A186 A212 D214 H216 E240 G265 E266 Q287 P288 E289 H315 T317 E341
• Catalytic site (residue number reindexed from 1): F181 A183 K185 A187 A213 D215 H217 E241 G266 E267 Q288 P289 E290 H316 T318 E342

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0003824 catalytic activity
• GO:0016853 isomerase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0009063 amino acid catabolic process

External links

• PDB: RCSB:4dn1, PDBe:4dn1, PDBj:4dn1
• PDBsum: 4dn1
• UniProt: A9CL63