Research workbench
Crystal structure of a peptide deformylase from burkholderia ambifaria with actinonin
Analyse Crystal structure of a peptide deformylase from burkholderia ambifaria with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I2B
- Type
- protein
- Length
- 167 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide deformylase
- EC
- 3.5.1.88
- UniProt
- B1FPK4
- Ligands
- BB2, ZN
- Pockets
- 1 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide deformylase (EC 3.5.1.88) | protein | 167 | 29% helix, 33% strand | B1FPK4 |
Ligands and binding sites
- BB2 · Actinonin · ligand · chains A
- ZN · Zinc ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.53 | 0.80 | 25 | BB2 |
Compared structures
- 5I2B · Crystal structure of a peptide deformylase from Burkholderia ambifaria with actinonin · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt B1FPK4
- Elsewhere: RCSB PDB 5I2B · PDBe 5I2B · UniProt B1FPK4
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