MolNFT v1 · #46972 · protein
Crystal structure of peptide deformylase 2 with actinonin from bacillus cereus
2OKL: “Crystal structure of peptide deformylase 2 with actinonin from bacillus cereus”. X-ray diffraction, 2 ligands (BB2, ZN), 1 pocket (best druggability 0.80). MolNFT v1 #46972 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2OKL
- Type
- protein
- Length
- 369 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide deformylase 2
- EC
- 3.5.1.88
- UniProt
- Q819K2
- Ligands
- BB2, ZN
- Pockets
- 1 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide deformylase 2 (EC 3.5.1.88) | protein | 185 | 28% helix, 26% strand | Q819K2 |
| B | Peptide deformylase 2 (EC 3.5.1.88) | protein | 184 | 28% helix, 28% strand | Q819K2 |
Ligands and binding sites
- BB2 · Actinonin · ligand · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CIT · Citric acid · additive · 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 | 1184 | 0.80 | 0.82 | 89 | BB2 |
Interfaces
1 interface between chains.
- A–B · 1041 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2OKL · Crystal structure of Peptide Deformylase 2 with actinonin from Bacillus cereus · the same entry in another collection · chain A against A, TM-score 1.00
- Q819K2 · AlphaFold monomer V2.0 prediction for peptide deformylase 2 (Q819K2) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q819K2
- Elsewhere: RCSB PDB 2OKL · PDBe 2OKL · UniProt Q819K2
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