MolNFT v1 · #2321 · protein
Peptide deformylase as FE2+ containing form (native) in complex with inhibitor polyethylene glycol
1BSZ · Protein (peptide deformylase): “Peptide deformylase as FE2+ containing form (native) in complex with inhibitor polyethylene glycol”. X-ray diffraction, 2 ligands (FE, SO4), 4 pockets (best druggability 0.57). MolNFT v1 #2321 on…
- PDB
- 1BSZ
- Type
- protein
- Length
- 504 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (peptide deformylase)
- EC
- 3.5.1.31
- UniProt
- P0A6K3
- Ligands
- FE, SO4
- Pockets
- 4 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Protein (peptide deformylase) (EC 3.5.1.31) | protein | 168 | 36% helix, 24% strand | P0A6K3 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 2 copies · chains B, C
- 2PE · Nonaethylene glycol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 348 | 0.57 | 0.75 | 48 | FE, 2PE |
| 2 | 285 | 0.56 | 0.77 | 36 | 2PE |
| 3 | 151 | 0.51 | 0.79 | 24 | FE, 2PE |
| 4 | 69 | 0.29 | 0.73 | 16 | empty |
Interfaces
2 interfaces between chains.
- B–C · 626 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 277 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1BSZ · Peptide deformylase as FE2+ containing form (native) in complex with inhibitor… · 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 A 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 P0A6K3
- Elsewhere: RCSB PDB 1BSZ · PDBe 1BSZ · UniProt P0A6K3
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