MolNFT v1 · #32625 · protein
Iron-bound crystal structure of dps-like peroxide resistance protein (dpr) from streptococcus suis.
2BW1: “Iron-bound crystal structure of dps-like peroxide resistance protein (dpr) from streptococcus suis.”. X-ray diffraction, 2 ligands (FE, CA), 20 pockets (best druggability 0.68). MolNFT v1 #32625 on GenesisL1: 3D structure, binding…
- PDB
- 2BW1
- Type
- protein
- Length
- 1,829 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dps-like peroxide resistance protein
- UniProt
- Q9F5J9
- Ligands
- FE, CA
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F, H, I, J, L | Dps-like peroxide resistance protein | protein | 151 | 76% helix, 0% strand | Q9F5J9 |
| D | 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 |
| K | Dps-like peroxide resistance protein | protein | 153 | 75% helix, 0% strand | Q9F5J9 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 12 copies · chains A, C, B, D, E, G, F, H, I, K, J, L
- CA · Calcium ion · metal · chains K
- 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 | 209 | 0.68 | 0.85 | 31 | empty |
| 2 | 244 | 0.67 | 0.84 | 32 | empty |
| 3 | 139 | 0.67 | 0.88 | 25 | empty |
| 4 | 205 | 0.67 | 0.85 | 32 | empty |
| 5 | 232 | 0.66 | 0.84 | 31 | empty |
Interfaces
30 interfaces between chains.
- J–L · 1191 Ų buried · 19 hydrogen bonds · protein-protein
- E–G · 1182 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1181 Ų buried · 20 hydrogen bonds · protein-protein
- F–H · 1181 Ų buried · 20 hydrogen bonds · protein-protein
- I–K · 1180 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 2BW1 · Iron-bound crystal structure of 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 2BW1 · PDBe 2BW1 · UniProt Q9F5J9
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