MolNFT v1 · #57836 · protein
Crystal structure of the SEP22 dodecamer, a dps-like protein from salmonella enterica subsp. enterica serovar enteritidis
3AK8 · DNA protection during starvation protein: “Crystal structure of the SEP22 dodecamer, a dps-like protein from salmonella enterica subsp. enterica serovar…”. X-ray diffraction, 2 ligands (MG, SO4), 20 pockets (best druggability 0.55).…
- PDB
- 3AK8
- Type
- protein
- Length
- 1,863 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA protection during starvation protein
- EC
- 1.16.-.-
- UniProt
- B3YEF4
- Ligands
- MG, SO4
- Pockets
- 20 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 73% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA protection during starvation protein (EC 1.16.-.-) | protein | 154 | 74% helix, 1% strand | B3YEF4 |
| B, C, D, E, G, H, I, J, K, L | DNA protection during starvation protein (EC 1.16.-.-) | protein | 155 | 73% helix, 1% strand | B3YEF4 |
| F | DNA protection during starvation protein (EC 1.16.-.-) | protein | 159 | 72% helix, 1% strand | B3YEF4 |
Ligands and binding sites
- MG · Magnesium ion · metal · 15 copies · chains A, E, I, C, B, G, L, D, H, F, K, J
- SO4 · Sulfate ion · ion · 6 copies · chains A, C, B, D, F, H, E, G, I, K, J, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 263 | 0.55 | 0.77 | 26 | MG |
| 2 | 261 | 0.54 | 0.77 | 25 | MG |
| 3 | 258 | 0.54 | 0.76 | 22 | MG |
| 4 | 261 | 0.53 | 0.76 | 21 | MG |
| 5 | 89 | 0.44 | 0.80 | 19 | SO4 |
Interfaces
30 interfaces between chains.
- B–D · 1605 Ų buried · 18 hydrogen bonds · protein-protein
- F–H · 1602 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1585 Ų buried · 22 hydrogen bonds · protein-protein
- E–G · 1580 Ų buried · 20 hydrogen bonds · protein-protein
- J–L · 1574 Ų buried · 19 hydrogen bonds · protein-protein
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 B3YEF4
- Elsewhere: RCSB PDB 3AK8 · PDBe 3AK8 · UniProt B3YEF4
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