Research workbench
Crystal structure of the DNA-binding transcriptional repressor deor from escherichia COLI str. K-12
Analyse Crystal structure of the DNA-binding transcriptional repressor deor from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L6L
- Type
- protein
- Length
- 1,078 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyribose operon repressor
- UniProt
- P0ACK5
- Ligands
- SO4, CL
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, F | Deoxyribose operon repressor | protein | 179 | 35% helix, 27% strand | P0ACK5 |
| B | Deoxyribose operon repressor | protein | 183 | 37% helix, 27% strand | P0ACK5 |
| D | Deoxyribose operon repressor | protein | 180 | 34% helix, 27% strand | P0ACK5 |
| E | Deoxyribose operon repressor | protein | 178 | 35% helix, 28% strand | P0ACK5 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 20 copies · chains A, E, B, C, D, F
- CL · Chloride ion · ion · 4 copies · chains B, C, E, F
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1159 | 0.75 | 0.78 | 85 | SO4 |
| 2 | 82 | 0.54 | 0.85 | 18 | CL |
| 3 | 58 | 0.48 | 0.85 | 18 | empty |
| 4 | 103 | 0.47 | 0.81 | 18 | SO4 |
| 5 | 118 | 0.45 | 0.79 | 20 | SO4 |
Interfaces
10 interfaces between chains.
- C–E · 951 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 943 Ų buried · 11 hydrogen bonds · protein-protein
- B–F · 902 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 521 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 520 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 7L6L · Crystal Structure of the DNA-binding Transcriptional Repressor DeoR from Escherichia coli… · the same entry in another collection · chain F against F, TM-score 1.00
- P0ACK5 · AlphaFold monomer V2.0 prediction for deoxyribose operon repressor (P0ACK5) · a predicted model of the same protein · chain E against A, TM-score 0.99
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 P0ACK5
- Elsewhere: RCSB PDB 7L6L · PDBe 7L6L · UniProt P0ACK5
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