Structure of PDB 6qkb Chain A Binding Site BS02

Receptor Information

>6qkb Chain A (length=384) Species: 266 (Paracoccus denitrificans)

KTDFSGYEVGYDIPALPGMDESEIQTPCLILDLDALERNIRKMGDYAKAH
GMRHRSHGKMHKSVDVQKLQESLGGSVGVCCQKVSEAEAFARGGIKDVLV
TNEVREPAKIDRLARLPKTGATVTVCVDDVQNIADLSAAAQKHGTELGIF
VEIDCGAGRCGVTTKEAVVEIAKAAAAAPNLTFKGIQAYQGAMQHMDSFE
DRKAKLDAAIAQVKEAVDALEAEGLAPEFVSGGGTGSYYFESNSGIYNEL
QCGSYAFMDADYGRIHDAEGKRIDQGEWENALFILTSVMSHAKPHLAVVD
AGLKAQSVDSGLPFVYGRDDVKYIKCSDEHGVVEDKDGVLKVNDKLRLVP
GHCDPTCNVHDWYVGVRNGKVETVWPVSARGKGY

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: 6qkb Chain A Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6qkb Marine Proteobacteria metabolize glycolate via the beta-hydroxyaspartate cycle.
• Resolution: 1.701 Å
• Binding residue (original residue number in PDB): H355 D357
• Binding residue (residue number reindexed from 1): H352 D354
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 4.1.3.41: 3-hydroxy-D-aspartate aldolase.

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0008721 D-serine ammonia-lyase activity
• GO:0016829 lyase activity
• GO:0016833 oxo-acid-lyase activity
• GO:0030170 pyridoxal phosphate binding
• GO:0046872 metal ion binding

Biological Process

• GO:0009436 glyoxylate catabolic process
• GO:0036088 D-serine catabolic process
• GO:0046296 glycolate catabolic process

External links

• PDB: RCSB:6qkb, PDBe:6qkb, PDBj:6qkb
• PDBsum: 6qkb
• PubMed: 31723261
• UniProt: A1B8Z1|BHCC_PARDP 3-hydroxy-D-aspartate aldolase (Gene Name=bhcC)