MolNFT v1 · #120587 · protein + DNA
Structural and dynamics studies of the tetr family protein, cprb from streptomyces coelicolor in complex with its biological operator sequence
5H58: “Structural and dynamics studies of the tetr family protein, cprb from streptomyces coelicolor in complex with…”. X-ray diffraction, 12 pockets (best druggability 0.90). MolNFT v1 #120587 on GenesisL1: 3D structure, binding sites and…
- 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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