Structure of PDB 2hzl Chain B Binding Site BS03

Receptor Information

>2hzl Chain B (length=337) Species: 272943 (Cereibacter sphaeroides 2.4.1)

APKVTWRLASSFPKSLDTIFGGAEVLSKMLSEATDGNFQIQVFSAGELVP
GLQAADAVTEGTVECCHTVGYYYWGKDPTFALAAAVPFSLSARGINAWHY
HGGGIDLYNEFLSQHNIVAFPGGNTGVQMGGWFRREINTVADMQGLKMRV
GGFAGKVMERLGVVPQQIAGGDIYPALEKGTIDATEWVGPYDDEKLGFFK
VAPYYYYPGWWEGGPTVHFMFNKSAYEGLTPTYQSLLRTACHAADANMLQ
LYDWKNPTAIKSLVAQGTQLRPFSPEILQACFEAANEVYAEMEASNPAFK
KIWDSIKAFRSEHYTWAQIAEYNYDTFMMVQQNAGKL

Ligand information

• Ligand ID: PYR
• InChI: InChI=1S/C3H4O3/c1-2(4)3(5)6/h1H3,(H,5,6)
• InChIKey: LCTONWCANYUPML-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.385: CC(=O)C(O)=O
  OpenEye OEToolkits 1.7.6: CC(=O)C(=O)O
  ACDLabs 12.01: O=C(C(=O)O)C
• Formula: C3 H4 O3
• Name: PYRUVIC ACID
• ChEMBL: CHEMBL1162144
• DrugBank: DB00119
• ZINC: ZINC000001532517
• PDB chain: 2hzl Chain B Residue 603

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2hzl Crystal structures of an Extracytoplasmic Solute Receptor from a TRAP transporter in its open and closed forms reveal a helix-swapped dimer requiring a cation for alpha-keto acid binding.
• Resolution: 1.4 Å
• Binding residue (original residue number in PDB): F116 F310 N314 Y317 R338
• Binding residue (residue number reindexed from 1): F88 F282 N286 Y289 R310
• Annotation score: 4
• Binding affinity: MOAD: Kd=270nM

Gene Ontology

Molecular Function

• GO:0043177 organic acid binding

Biological Process

• GO:0015849 organic acid transport
• GO:0055085 transmembrane transport

Cellular Component

• GO:0031317 tripartite ATP-independent periplasmic transporter complex

External links

• PDB: RCSB:2hzl, PDBe:2hzl, PDBj:2hzl
• PDBsum: 2hzl
• PubMed: 17362499
• UniProt: Q3J1R2|TAKP_CERS4 Alpha-keto acid-binding periplasmic protein TakP (Gene Name=takP)