Research workbench
Structural and dynamics studies of the tetr family protein, cprb from streptomyces coelicolor in complex with its biological operator sequence
Analyse Structural and dynamics studies of the tetr family protein, cprb from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5H58
- Type
- protein + DNA
- Length
- 833 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cprb; DNA (5'- D(*AP*GP*GP*C*AP*GP*GP*CP*GP*GP*CP*AP*CP*GP*GP*TP*CP*TP*GP*TP*TP*GP*A…
- UniProt
- O66122
- Pockets
- 12 · best druggability 0.90
Structure
x-ray diffraction · 6 distinct chains · 48% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cprb | protein | 194 | 51% helix, 0% strand | O66122 |
| B | Cprb | protein | 204 | 42% helix, 0% strand | O66122 |
| C | Cprb | protein | 200 | 53% helix, 0% strand | O66122 |
| D | Cprb | protein | 193 | 46% helix, 0% strand | O66122 |
| E | DNA (5'- D(*AP*GP*GP*C*AP*GP*GP*CP*GP*GP*CP*AP*CP*GP*GP*TP*CP*TP*GP*TP*TP*GP*A P*GP*TP*TP*C)-3') | dna | 20 | — | — |
| F | DNA (5'- D(*GP*AP*A*CP*TP*CP*AP*AP*CP*AP*GP*AP*CP*CP*GP*TP*GP*CP*CP*GP*CP*CP*T P*GP*CP*CP*T)-3') | dna | 22 | — | — |
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1177 | 0.90 | 0.91 | 122 | empty |
| 2 | 1139 | 0.88 | 0.89 | 128 | empty |
| 3 | 253 | 0.75 | 0.89 | 49 | empty |
| 4 | 230 | 0.51 | 0.76 | 25 | empty |
| 5 | 92 | 0.51 | 0.83 | 25 | empty |
Interfaces
11 interfaces between chains.
- C–D · 1249 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1183 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 971 Ų buried · 70 hydrogen bonds · nucleic-nucleic
- C–F · 531 Ų buried · 6 hydrogen bonds · protein-nucleic
- C–E · 443 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5H58 · Structural and dynamics studies of the TetR family protein, CprB from Streptomyces… · 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 O66122
- Elsewhere: RCSB PDB 5H58 · PDBe 5H58 · UniProt O66122
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