Structure of PDB 4dz4 Chain D Binding Site BS02

Receptor Information

>4dz4 Chain D (length=317) Species: 271848 (Burkholderia thailandensis E264)

ETLYGDGAIRRPSVYGSSIENTYAGVLSFMRRNYTRDLDGVDVVVSGVPL
DLATTFRSGARLGPSAVRAASVQLAELNPYPWGFDPFDDLAVIDYGDCWF
DAHHPLSIKPAIVEHARTILQSDARMLTLGGDHYITYPLLIAHAQKYGKP
LSLIHFDAHCDTWADDADSLNHGTMFYKAVKDGLIDPKASVQVGIRTWND
DYLGINVLDAAWVHEHGARATLERIESIVGGRPAYLTFDIDCLDPAFAPG
TGTPVAGGLSSAQALAIVRGLGGVNLIGADVVEVAPAYDQSEITAIAAAH
VACDLLCLWRQRKAGAR

Ligand information

• Ligand ID: MN
• InChI: InChI=1S/Mn/q+2
• InChIKey: WAEMQWOKJMHJLA-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mn+2]
  CACTVS 3.341: [Mn++]
• Formula: Mn
• Name: MANGANESE (II) ION
• DrugBank: DB06757
• PDB chain: 4dz4 Chain D Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4dz4 Combining functional and structural genomics to sample the essential Burkholderia structome.
• Resolution: 1.7 Å
• Binding residue (original residue number in PDB): H135 D159 D163 D242
• Binding residue (residue number reindexed from 1): H133 D157 D161 D239
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): H135 D159 H161 D163 H175 D242 D244 E286
• Catalytic site (residue number reindexed from 1): H133 D157 H159 D161 H172 D239 D241 E283
• Enzyme Commision number: 3.5.3.11: agmatinase.

Gene Ontology

Molecular Function

• GO:0008783 agmatinase activity
• GO:0016787 hydrolase activity
• GO:0016813 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines
• GO:0046872 metal ion binding

Biological Process

• GO:0033389 putrescine biosynthetic process from arginine, using agmatinase

External links

• PDB: RCSB:4dz4, PDBe:4dz4, PDBj:4dz4
• PDBsum: 4dz4
• PubMed: 23382856
• UniProt: Q2T3W4