Research workbench
Crystal structure of peptide deformylase from leptospira interrogans (lipdf) at PH7.5
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
- 1SV2
- Type
- protein
- Length
- 343 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
- 5 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide deformylase (EC 3.5.1.88) | protein | 171 | 26% helix, 30% strand | Q93LE9 |
| B | Peptide deformylase (EC 3.5.1.88) | protein | 172 | 27% helix, 35% strand | Q93LE9 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 2 copies · chains A, B
- FMT · Formic acid · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.71 | 0.97 | 17 | DTT |
| 2 | 54 | 0.70 | 0.97 | 16 | DTT |
| 3 | 422 | 0.60 | 0.76 | 52 | empty |
| 4 | 93 | 0.35 | 0.74 | 17 | empty |
| 5 | 66 | 0.29 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 489 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1SV2 · Crystal Structure of Peptide Deformylase from Leptospira Interrogans (LiPDF) at pH7.5 · 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 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 Q93LE9
- Elsewhere: RCSB PDB 1SV2 · PDBe 1SV2 · UniProt Q93LE9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.