Research workbench
Crystal structure of peptide deformylase from leptospira interrogans (lipdf) at PH6.5
Analyse Crystal structure of peptide deformylase from leptospira interrogans (lipdf) at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VEV
- Type
- protein
- Length
- 342 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide deformylase
- EC
- 3.5.1.88
- UniProt
- Q93LE9
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peptide deformylase (EC 3.5.1.88) | protein | 171 | 29% helix, 30% strand | Q93LE9 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 3 copies · chains A, B
- FMT · Formic acid · additive · 2 copies · chains A, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.74 | 0.99 | 17 | MES, FMT |
| 2 | 68 | 0.73 | 0.98 | 18 | MES, FMT |
| 3 | 66 | 0.31 | 0.74 | 16 | empty |
Compared structures
- 1VEV · Crystal structure of peptide deformylase from Leptospira Interrogans (LiPDF) at pH6.5 · the same entry in another collection · chain A against A, TM-score 1.00
- Q93LE9 · AlphaFold monomer V2.0 prediction for peptide deformylase (Q93LE9) · a predicted model of the same protein · chain B 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 Q93LE9
- Elsewhere: RCSB PDB 1VEV · PDBe 1VEV · UniProt Q93LE9
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