Research workbench
Identification of two zinc-binding sites in the Streptococcus suis Dpr protein
Analyse Identification of two zinc-binding sites in the Streptococcus suis Dpr protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2UX1
- Type
- protein
- Length
- 1,833 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- STREPTOCOCCUS SUIS
- Molecule
- DNA protection during starvation protein
- EC
- 1.16.-.-
- UniProt
- Q9F5J9
- Ligands
- ZN, CA, CL
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · resolution 1.8 · 5 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | DNA protection during starvation protein (EC 1.16.-.-) | protein | 151 | 75% helix, 0% strand | Q9F5J9 |
| D, F, H, J, K, L | DNA protection during starvation protein (EC 1.16.-.-) | protein | 152 | 76% helix, 0% strand | Q9F5J9 |
| E | DNA protection during starvation protein (EC 1.16.-.-) | protein | 150 | 75% helix, 0% strand | Q9F5J9 |
| G | DNA protection during starvation protein (EC 1.16.-.-) | protein | 165 | 69% helix, 0% strand | Q9F5J9 |
| I | DNA protection during starvation protein (EC 1.16.-.-) | protein | 153 | 75% helix, 0% strand | Q9F5J9 |
Ligands and binding sites
- ZN · Zinc ion · metal · 24 copies · chains A, C, B, D, E, G, F, H, I, K, J, L
- CA · Calcium ion · metal · 4 copies · chains D, H, I, K
- CL · Chloride ion · ion · 2 copies · chains H, C, L
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains C, E, L, D, G, I, B, F, J, 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 | 239 | 0.71 | 0.86 | 32 | ZN |
| 2 | 245 | 0.71 | 0.86 | 34 | ZN |
| 3 | 263 | 0.70 | 0.85 | 35 | ZN |
| 4 | 206 | 0.70 | 0.87 | 30 | ZN |
| 5 | 225 | 0.69 | 0.86 | 34 | ZN |
Interfaces
30 interfaces between chains.
- E–G · 1210 Ų buried · 19 hydrogen bonds · protein-protein
- J–L · 1180 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 1177 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1175 Ų buried · 20 hydrogen bonds · protein-protein
- F–H · 1169 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 2UX1 · Identification of two zinc-binding sites in the streptococcus suis dpr protein · 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 2UX1 · PDBe 2UX1 · UniProt Q9F5J9
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