Research workbench
Crystal structure of E. COLI dps in space group P1
Analyse Crystal structure of E. COLI dps in space group P1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AQS
- Type
- protein
- Length
- 3,756 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA protection during starvation protein
- EC
- 1.16.-.-
- UniProt
- P0ABT2
- Ligands
- FE
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 72% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, H, I, K, M, P, S, T, U, V, W | DNA protection during starvation protein (EC 1.16.-.-) | protein | 156 | 73% helix, 1% strand | P0ABT2 |
| C, O | DNA protection during starvation protein (EC 1.16.-.-) | protein | 157 | 73% helix, 1% strand | P0ABT2 |
| E, G, L, Q | DNA protection during starvation protein (EC 1.16.-.-) | protein | 159 | 72% helix, 1% strand | P0ABT2 |
| F, J, N, R | DNA protection during starvation protein (EC 1.16.-.-) | protein | 155 | 74% helix, 1% strand | P0ABT2 |
| X | DNA protection during starvation protein (EC 1.16.-.-) | protein | 158 | 72% helix, 1% strand | P0ABT2 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 24 copies · chains A, C, B, D, E, G, F, H, I, K, J, L, M, O, N, P, Q, S, R, T, U, W, V, X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.70 | 0.97 | 21 | empty |
| 2 | 575 | 0.64 | 0.75 | 55 | empty |
| 3 | 457 | 0.63 | 0.77 | 41 | empty |
| 4 | 251 | 0.56 | 0.78 | 22 | empty |
| 5 | 261 | 0.56 | 0.77 | 22 | empty |
Interfaces
62 interfaces between chains.
- Q–S · 1632 Ų buried · 20 hydrogen bonds · protein-protein
- V–X · 1627 Ų buried · 19 hydrogen bonds · protein-protein
- E–G · 1614 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1612 Ų buried · 17 hydrogen bonds · protein-protein
- U–W · 1612 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 72 modified (engineered).
Compared structures
- 7AQS · Crystal structure of E. coli DPS in space group P1 · the same entry in another collection · chain G against G, 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 P0ABT2
- Elsewhere: RCSB PDB 7AQS · PDBe 7AQS · UniProt P0ABT2
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