Research workbench
X-ray structure dps from kineococcus radiotolerans in complex with mn (II) ions.
Analyse X-ray structure dps from kineococcus radiotolerans in complex with mn (II) ions. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4A25
- Type
- protein
- Length
- 671 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferritin dps family protein
- UniProt
- A6WG04
- Ligands
- MN, CL
- Pockets
- 2 · best druggability 0.51
Structure
x-ray diffraction · 3 distinct chains · 72% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ferritin dps family protein | protein | 167 | 72% helix, 2% strand | A6WG04 |
| B, C | Ferritin dps family protein | protein | 169 | 71% helix, 2% strand | A6WG04 |
| D | Ferritin dps family protein | protein | 166 | 72% helix, 2% strand | A6WG04 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 10 copies · chains A, B, C, D
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 143 | 0.51 | 0.80 | 27 | empty |
| 2 | 57 | 0.38 | 0.80 | 13 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1348 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1346 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1221 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 674 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 22 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4A25 · X-ray structure Dps from Kineococcus radiotolerans in complex with Mn (II) ions. · 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 A6WG04
- Elsewhere: RCSB PDB 4A25 · PDBe 4A25 · UniProt A6WG04
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