Research workbench
An E. COLI dps protein from ferritin superfamily
Analyse An E. COLI dps protein from ferritin superfamily in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6B0D
- Type
- protein
- Length
- 941 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA protection during starvation protein
- EC
- 1.16.-.-
- UniProt
- P0ABT3
- Ligands
- NA
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 72% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA protection during starvation protein (EC 1.16.-.-) | protein | 161 | 71% helix, 1% strand | P0ABT3 |
| B, F | DNA protection during starvation protein (EC 1.16.-.-) | protein | 155 | 73% helix, 1% strand | P0ABT3 |
| C, E | DNA protection during starvation protein (EC 1.16.-.-) | protein | 157 | 72% helix, 1% strand | P0ABT3 |
| D | DNA protection during starvation protein (EC 1.16.-.-) | protein | 156 | 72% helix, 1% strand | P0ABT3 |
Ligands and binding sites
- NA · Sodium ion · metal · 12 copies · chains A, D, E, B, C, F
- FMT · Formic acid · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.73 | 0.98 | 20 | empty |
| 2 | 109 | 0.67 | 0.90 | 24 | empty |
| 3 | 261 | 0.58 | 0.78 | 22 | empty |
| 4 | 109 | 0.37 | 0.75 | 24 | NA |
| 5 | 86 | 0.37 | 0.76 | 21 | empty |
Interfaces
10 interfaces between chains.
- A–F · 1624 Ų buried · 22 hydrogen bonds · protein-protein
- C–E · 1548 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 752 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 748 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 734 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6B0D · An E. coli DPS protein from ferritin superfamily · the same entry in another collection · chain F against F, TM-score 1.00
- P0ABT3 · AlphaFold monomer V2.0 prediction for DNA protection during starvation protein (P0ABT3) · a predicted model of the same protein · chain F 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 P0ABT3
- Elsewhere: RCSB PDB 6B0D · PDBe 6B0D · UniProt P0ABT3
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