MolNFT v1 · #57837 · protein
Crystal structure of the SEP22 dodecamer, a dps-like protein from salmonella enterica subsp. enterica serovar enteritidis, fe-soaked form
3AK9 · DNA protection during starvation protein: “Crystal structure of the SEP22 dodecamer, a dps-like protein from salmonella enterica subsp. enterica serovar…”. X-ray diffraction, 3 ligands (FE2, MG, SO4), 20 pockets (best druggability…
- PDB
- 3AK9
- Type
- protein
- Length
- 1,859 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
- FE2, MG, SO4
- Pockets
- 20 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 74% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F, G, H, I, J, K, L | DNA protection during starvation protein (EC 1.16.-.-) | protein | 155 | 74% helix, 1% strand | B3YEF4 |
| D | DNA protection during starvation protein (EC 1.16.-.-) | protein | 154 | 74% helix, 1% strand | B3YEF4 |
Ligands and binding sites
- FE2 · Fe (II) ion · metal · 12 copies · chains A, C, B, D, E, G, F, H, I, K, J, L
- MG · Magnesium ion · metal · 4 copies · chains D, F, K, B, G, L, C, H, J, A, E, I
- SO4 · Sulfate ion · ion · 6 copies · chains A, C, B, D, E, G, F, H, J, L, I, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 277 | 0.56 | 0.77 | 23 | MG |
| 2 | 260 | 0.55 | 0.77 | 24 | MG |
| 3 | 240 | 0.52 | 0.76 | 22 | MG |
| 4 | 237 | 0.52 | 0.76 | 25 | MG |
| 5 | 183 | 0.48 | 0.77 | 32 | empty |
Interfaces
30 interfaces between chains.
- I–K · 1635 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 1626 Ų buried · 23 hydrogen bonds · protein-protein
- E–G · 1624 Ų buried · 23 hydrogen bonds · protein-protein
- J–L · 1618 Ų buried · 24 hydrogen bonds · protein-protein
- F–H · 1597 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 3AK9 · Crystal structure of the SEp22 dodecamer, a Dps-like protein from Salmonella enterica… · 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 B3YEF4
- Elsewhere: RCSB PDB 3AK9 · PDBe 3AK9 · UniProt B3YEF4
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