Research workbench
Crystal structure of a peptide deformylase from synechococcus elongatus in complex with actinonin
Analyse Crystal structure of a peptide deformylase from synechococcus elongatus in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DR9
- Type
- protein
- Length
- 732 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide deformylase
- EC
- 3.5.1.88
- UniProt
- Q5N5L5
- Ligands
- BB2, ZN, BR
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide deformylase (EC 3.5.1.88) | protein | 182 | 30% helix, 26% strand | Q5N5L5 |
| B | Peptide deformylase (EC 3.5.1.88) | protein | 182 | 30% helix, 26% strand | Q5N5L5 |
| C, D | Peptide deformylase (EC 3.5.1.88) | protein | 184 | 29% helix, 27% strand | Q5N5L5 |
Ligands and binding sites
- BB2 · Actinonin · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- BR · Bromide ion · ion · 5 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 509 | 0.70 | 0.80 | 53 | BB2 |
| 2 | 519 | 0.68 | 0.78 | 55 | BB2 |
| 3 | 327 | 0.57 | 0.76 | 47 | BR |
| 4 | 340 | 0.57 | 0.76 | 50 | BR |
| 5 | 124 | 0.49 | 0.80 | 22 | BB2 |
Interfaces
5 interfaces between chains.
- C–D · 570 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 499 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 456 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 453 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 126 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4DR9 · Crystal structure of a peptide deformylase from synechococcus elongatus in complex with… · 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 Q5N5L5
- Elsewhere: RCSB PDB 4DR9 · PDBe 4DR9 · UniProt Q5N5L5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.