MolNFT v1 · #25078 · protein
Crystal structure of peptide deformylase from leptospira interrogans (lipdf) at PH7.0
1VEY: “Crystal structure of peptide deformylase from leptospira interrogans (lipdf) at PH7.0”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.66). MolNFT v1 #25078 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1VEY
- 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
- 4 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peptide deformylase (EC 3.5.1.88) | protein | 171 | 28% helix, 28% strand | Q93LE9 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 102 | 0.66 | 0.90 | 23 | ZN, EPE |
| 2 | 100 | 0.66 | 0.90 | 22 | EPE |
| 3 | 68 | 0.31 | 0.74 | 13 | empty |
| 4 | 69 | 0.31 | 0.74 | 16 | empty |
Compared structures
- 1VEY · Crystal Structure of Peptide Deformylase from Leptospira Interrogans (LiPDF) at pH7.0 · 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 0.98
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 Q93LE9
- Elsewhere: RCSB PDB 1VEY · PDBe 1VEY · UniProt Q93LE9
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