Research workbench
Crystal structure of lipdf
Analyse Crystal structure of lipdf in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y6H
- Type
- protein
- Length
- 354 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
- GLY, ZN
- Pockets
- 4 · best druggability 0.48
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peptide deformylase (EC 3.5.1.88) | protein | 177 | 29% helix, 32% strand | Q93LE9 |
Ligands and binding sites
- GLY · Glycine · ligand · chains B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- FMT · Formic acid · additive · 8 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 144 | 0.48 | 0.78 | 23 | FMT |
| 2 | 95 | 0.37 | 0.75 | 18 | empty |
| 3 | 76 | 0.32 | 0.74 | 15 | empty |
| 4 | 63 | 0.29 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 961 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
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 1Y6H · PDBe 1Y6H · UniProt Q93LE9
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