MolNFT v1 · #13910 · protein
Crystal structure of E.COLI peptide deformylase complexed with antibiotic actinonin
1LRU: “Crystal structure of E.COLI peptide deformylase complexed with antibiotic actinonin”. X-ray diffraction, 3 ligands (BB2, ZN, SO4), 3 pockets (best druggability 0.56). MolNFT v1 #13910 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1LRU
- Type
- protein
- Length
- 489 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide deformylase
- EC
- 3.5.1.88
- UniProt
- P0A6K3
- Ligands
- BB2, ZN, SO4
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peptide deformylase (EC 3.5.1.88) | protein | 164 | 32% helix, 28% strand | P0A6K3 |
| C | Peptide deformylase (EC 3.5.1.88) | protein | 161 | 32% helix, 33% strand | P0A6K3 |
Ligands and binding sites
- BB2 · Actinonin · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.56 | 0.80 | 23 | BB2 |
| 2 | 152 | 0.49 | 0.78 | 24 | BB2 |
| 3 | 135 | 0.48 | 0.79 | 24 | ZN, BB2 |
Compared structures
- 1LRU · Crystal Structure of E.coli Peptide Deformylase Complexed with Antibiotic Actinonin · the same entry in another collection · chain A against A, TM-score 1.00
- P0A6K3 · AlphaFold monomer V2.0 prediction for peptide deformylase (P0A6K3) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P0A6K3
- Elsewhere: RCSB PDB 1LRU · PDBe 1LRU · UniProt P0A6K3
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