Research workbench
Dpsc from streptomyces coelicolor
Analyse Dpsc from streptomyces coelicolor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CYB
- Type
- protein
- Length
- 2,062 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative DNA protection protein
- UniProt
- Q9K3L0
- Ligands
- FE, NA
- Pockets
- 20 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 69% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, F, G, H, I, L | Putative DNA protection protein | protein | 172 | 69% helix, 3% strand | Q9K3L0 |
| D, E, K | Putative DNA protection protein | protein | 171 | 69% helix, 2% strand | Q9K3L0 |
| J | Putative DNA protection protein | protein | 173 | 69% helix, 3% strand | Q9K3L0 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- NA · Sodium ion · metal · 4 copies · chains C, F, H, G, B, D, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 237 | 0.59 | 0.80 | 26 | empty |
| 2 | 175 | 0.58 | 0.82 | 26 | empty |
| 3 | 208 | 0.58 | 0.80 | 23 | empty |
| 4 | 83 | 0.57 | 0.87 | 22 | empty |
| 5 | 188 | 0.56 | 0.81 | 24 | empty |
Interfaces
30 interfaces between chains.
- A–B · 2021 Ų buried · 32 hydrogen bonds · protein-protein
- I–J · 2009 Ų buried · 33 hydrogen bonds · protein-protein
- G–H · 2008 Ų buried · 33 hydrogen bonds · protein-protein
- E–F · 1965 Ų buried · 32 hydrogen bonds · protein-protein
- K–L · 1963 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 4CYB · DpsC from Streptomyces coelicolor · 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 Q9K3L0
- Elsewhere: RCSB PDB 4CYB · PDBe 4CYB · UniProt Q9K3L0
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