MolNFT v1 · #24171 · protein
Crystal structure of dps-like peroxide resistance protein (dpr) from streptococcus suis
1UMN: “Crystal structure of dps-like peroxide resistance protein (dpr) from streptococcus suis”. X-ray diffraction, 2 ligands (CA, CL), 20 pockets (best druggability 0.74). MolNFT v1 #24171 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1UMN
- Type
- protein
- Length
- 1,832 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dps-like peroxide resistance protein
- UniProt
- Q9F5J9
- Ligands
- CA, CL
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, F, H, L | Dps-like peroxide resistance protein | protein | 151 | 76% helix, 0% strand | Q9F5J9 |
| D, E, J, K | Dps-like peroxide resistance protein | protein | 152 | 75% helix, 0% strand | Q9F5J9 |
| G | Dps-like peroxide resistance protein | protein | 165 | 68% helix, 0% strand | Q9F5J9 |
| I | Dps-like peroxide resistance protein | protein | 153 | 75% helix, 0% strand | Q9F5J9 |
Ligands and binding sites
- CA · Calcium ion · metal · 16 copies · chains A, B, C, D, E, F, H, G, I, K, J, L
- CL · Chloride ion · ion · 3 copies · chains D, H, I
- 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 | 222 | 0.74 | 0.89 | 31 | CA |
| 2 | 243 | 0.74 | 0.88 | 37 | CA |
| 3 | 246 | 0.73 | 0.88 | 33 | CA |
| 4 | 244 | 0.73 | 0.88 | 35 | CA |
| 5 | 216 | 0.72 | 0.88 | 33 | CA |
Interfaces
30 interfaces between chains.
- J–L · 1194 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1180 Ų buried · 14 hydrogen bonds · protein-protein
- F–H · 1180 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 1179 Ų buried · 14 hydrogen bonds · protein-protein
- I–K · 1172 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1UMN · Crystal structure of Dps-like peroxide resistance protein (Dpr) from Streptococcus suis · 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 1UMN · PDBe 1UMN · UniProt Q9F5J9
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