Research workbench
Structure of the DNA-binding domain of E. COLI proline utilization a (puta)
Analyse Structure of the DNA-binding domain of E. COLI proline utilization a (puta) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GPE
- Type
- protein
- Length
- 187 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional protein puta
- UniProt
- P09546
- Pockets
- 1 · best druggability 0.36
Structure
x-ray diffraction · 3 distinct chains · 64% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional protein puta | protein | 47 | 64% helix, 19% strand | P09546 |
| B, C | Bifunctional protein puta | protein | 46 | 65% helix, 20% strand | P09546 |
| D | Bifunctional protein puta | protein | 48 | 63% helix, 19% strand | P09546 |
Ligands and binding sites
- IMD · Imidazole · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 120 | 0.36 | 0.73 | 19 | IMD |
Interfaces
3 interfaces between chains.
- C–D · 1784 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1703 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 15 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2GPE · Structure of the DNA-binding domain of E. Coli Proline Utilization A (PUTA) · the same entry in another collection · chain B against B, TM-score 1.00
- P09546 · AlphaFold monomer V2.0 prediction for bifunctional protein puta (P09546) · a predicted model of the same protein · chain B against A, TM-score 0.80
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 P09546
- Elsewhere: RCSB PDB 2GPE · PDBe 2GPE · UniProt P09546
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