Research workbench
Crystal structure of type 2 pdf from streptococcus agalactiae in complex with inhibitor AT002
Analyse Crystal structure of type 2 pdf from streptococcus agalactiae in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JF2
- Type
- protein
- Length
- 203 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide deformylase
- EC
- 3.5.1.88
- UniProt
- Q8E378
- Ligands
- SF7, ZN
- Pockets
- 1 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide deformylase (EC 3.5.1.88) | protein | 203 | 29% helix, 25% strand | Q8E378 |
Ligands and binding sites
- SF7 · (3R)-3-{3-[(4-fluorophenyl)methyl]-1,2,4-oxadiazol-5-yl}-N-hydroxyheptanamide · ligand · chains A
- ZN · Zinc ion · metal · 8 copies · chains A
- ACT · Acetate ion · additive · chains A
- IMD · Imidazole · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.53 | 0.82 | 22 | SF7 |
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 5JF2 · Crystal structure of type 2 PDF from Streptococcus agalactiae in complex with inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8E378 · AlphaFold monomer V2.0 prediction for peptide deformylase (Q8E378) · a predicted model of the same protein · chain A 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 Q8E378
- Elsewhere: RCSB PDB 5JF2 · PDBe 5JF2 · UniProt Q8E378
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