Research workbench
Crystal structure of peptide deformylase from leptospira interrogans complexed with inhibitor actinonin
Analyse Crystal structure of peptide deformylase from leptospira interrogans complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SZZ
- Type
- protein
- Length
- 1,368 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide deformylase
- EC
- 3.5.1.88
- UniProt
- Q93LE9
- Ligands
- BB2, ZN
- Pockets
- 13 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Peptide deformylase (EC 3.5.1.88) | protein | 171 | 29% helix, 24% strand | Q93LE9 |
Ligands and binding sites
- BB2 · Actinonin · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 362 | 0.65 | 0.79 | 38 | BB2 |
| 2 | 266 | 0.64 | 0.82 | 26 | BB2 |
| 3 | 273 | 0.64 | 0.81 | 26 | BB2 |
| 4 | 326 | 0.64 | 0.80 | 36 | BB2 |
| 5 | 340 | 0.63 | 0.79 | 34 | BB2 |
Interfaces
4 interfaces between chains.
- D–H · 796 Ų buried · 7 hydrogen bonds · protein-protein
- F–G · 792 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 776 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 770 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1SZZ · Crystal structure of peptide deformylase from Leptospira Interrogans complexed with… · the same entry in another collection · chain E against E, TM-score 1.00
- Q93LE9 · AlphaFold monomer V2.0 prediction for peptide deformylase (Q93LE9) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 Q93LE9
- Elsewhere: RCSB PDB 1SZZ · PDBe 1SZZ · UniProt Q93LE9
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