Research workbench
ASP74ALA mutant crystal structure for dps-like peroxide resistance protein dpr from streptococcus suis.
Analyse ASP74ALA mutant crystal structure for dps-like peroxide resistance protein dpr… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CF7
- Type
- protein
- Length
- 1,821 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dpr
- UniProt
- Q9F5J9
- Ligands
- CA, CL
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dpr | protein | 156 | 72% helix, 0% strand | Q9F5J9 |
| B | Dpr | protein | 150 | 76% helix, 0% strand | Q9F5J9 |
| C, D, I | Dpr | protein | 152 | 76% helix, 0% strand | Q9F5J9 |
| E, F, H, J, K, L | Dpr | protein | 151 | 75% helix, 0% strand | Q9F5J9 |
| G | Dpr | protein | 153 | 75% helix, 0% strand | Q9F5J9 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains J, K
- CL · Chloride ion · ion · 2 copies · chains J, K
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains B, F, J, C, E, L, D, G, I, A, H, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 191 | 0.74 | 0.90 | 31 | empty |
| 2 | 263 | 0.74 | 0.87 | 36 | empty |
| 3 | 248 | 0.73 | 0.87 | 38 | empty |
| 4 | 229 | 0.72 | 0.87 | 36 | empty |
| 5 | 254 | 0.72 | 0.86 | 41 | empty |
Interfaces
30 interfaces between chains.
- A–C · 1194 Ų buried · 14 hydrogen bonds · protein-protein
- E–G · 1171 Ų buried · 14 hydrogen bonds · protein-protein
- I–K · 1170 Ų buried · 14 hydrogen bonds · protein-protein
- F–H · 1153 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 1140 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 2CF7 · Asp74Ala mutant crystal structure for Dps-like peroxide resistance protein Dpr from… · 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 Q9F5J9
- Elsewhere: RCSB PDB 2CF7 · PDBe 2CF7 · UniProt Q9F5J9
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