Research workbench
Crystal structure of peptide deformylase from ehrlichia chaffeensis
Analyse Crystal structure of peptide deformylase from ehrlichia chaffeensis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OCA
- Type
- protein
- Length
- 358 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide deformylase
- EC
- 3.5.1.88
- UniProt
- Q2GI30
- Ligands
- ZN, CL
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide deformylase (EC 3.5.1.88) | protein | 179 | 32% helix, 28% strand | Q2GI30 |
| B | Peptide deformylase (EC 3.5.1.88) | protein | 179 | 33% helix, 28% strand | Q2GI30 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 889 | 0.79 | 0.81 | 92 | CL |
| 2 | 143 | 0.55 | 0.81 | 19 | empty |
| 3 | 126 | 0.52 | 0.81 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 610 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3OCA · Crystal structure of peptide deformylase from Ehrlichia chaffeensis · the same entry in another collection · chain A against A, TM-score 1.00
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 Q2GI30
- Elsewhere: RCSB PDB 3OCA · PDBe 3OCA · UniProt Q2GI30
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.