Structure of PDB 3k4d Chain A Binding Site BS01

Receptor Information

>3k4d Chain A (length=596) Species: 83333 (Escherichia coli K-12)

SHMLRPVETPTREIKKLDGLWAFSLDRENCGIDQRWWESALQESRAIAVP
GSFNDQFADADIRNYAGNVWYQREVFIPKGWAGQRIVLRFDAVTHYGKVW
VNNQEVMEHQGGYTPFEADVTPYVIAGKSVRITVCVNNELNWQTIPPGMV
ITDENGKKKQSYFHDFFNYAGIHRSVMLYTTPNTWVDDITVVTHVAQDCN
HASVDWQVVANGDVSVELRDADQQVVATGQGTSGTLQVVNPHLWQPGEGY
LYELCVTAKSQTECDIYPLRVGIRSVAVKGEQFLINHKPFYFTGFGRHED
ADLRGKGFDNVLMVHDHALMDWIGANSYRTSHYPYAEEMLDWADEHGIVV
IDETAAVGFNLSLGKPKELYSEEAVNGETQQAHLQAIKELIARDKNHPSV
VMWSIANEPDTRPQGAREYFAPLAEATRKLDPTRPITCVNVMFCDAHTDT
ISDLFDVLCLNRYYGWYVQSGDLETAEKVLEKELLAWQEKLHQPIIITEY
GVDTLAGLHSMYTDMWSEEYQCAWLDMYHRVFDRVSAVVGEQVWNFADFA
TSQGILRVGGNKKGIFTRDRKPKSAAFLLQKRWTGMNFGEKPQQGG

Ligand information

• Ligand ID: EVA
• InChI: InChI=1S/C6H9NO6/c8-2-1(6(12)13)7-5(11)4(10)3(2)9/h1-4,8-10H,(H,7,11)(H,12,13)/t1-,2+,3-,4+/m0/s1
• InChIKey: YEWOHTVJCCDCCS-NTAGLIMJSA-N
• SMILES:
  OpenEye OEToolkits 1.7.0: C1(C(C(NC(=O)C1O)C(=O)O)O)O
  OpenEye OEToolkits 1.7.0: [C@@H]1([C@@H]([C@H](NC(=O)[C@@H]1O)C(=O)O)O)O
  CACTVS 3.352: O[CH]1[CH](O)[CH](NC(=O)[CH]1O)C(O)=O
  ACDLabs 11.02: O=C(O)C1NC(=O)C(O)C(O)C1O
  CACTVS 3.352: O[C@H]1[C@H](O)[C@H](NC(=O)[C@@H]1O)C(O)=O
• Formula: C6 H9 N O6
• Name: (2S,3R,4S,5R)-3,4,5-trihydroxy-6-oxopiperidine-2-carboxylic acid
• ChEMBL: CHEMBL1232598
• PDB chain: 3k4d Chain A Residue 604

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3k4d Alleviating cancer drug toxicity by inhibiting a bacterial enzyme.
• Resolution: 2.393 Å
• Binding residue (original residue number in PDB): D163 H330 E413 Y468 Y472 E504 W549 K568
• Binding residue (residue number reindexed from 1): D165 H332 E408 Y463 Y467 E499 W544 K563
• Annotation score: 1
• Binding affinity: MOAD: Ki=7750nM
  PDBbind-CN: -logKd/Ki=5.11,Ki=7750nM
  BindingDB: Ki=232nM

Enzymatic activity

• Catalytic site (original residue number in PDB): D163 H296 H330 V355 F357 E413 Y468 E504 K568
• Catalytic site (residue number reindexed from 1): D165 H298 H332 V357 F359 E408 Y463 E499 K563
• Enzyme Commision number: 3.2.1.31: beta-glucuronidase.

Gene Ontology

Molecular Function

• GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
• GO:0004566 beta-glucuronidase activity
• GO:0016798 hydrolase activity, acting on glycosyl bonds
• GO:0030246 carbohydrate binding
• GO:0042802 identical protein binding

Biological Process

• GO:0005975 carbohydrate metabolic process

Cellular Component

• GO:0005829 cytosol
• GO:0032991 protein-containing complex

External links

• PDB: RCSB:3k4d, PDBe:3k4d, PDBj:3k4d
• PDBsum: 3k4d
• PubMed: 21051639
• UniProt: P05804|BGLR_ECOLI Beta-glucuronidase (Gene Name=uidA)