Research workbench
Elucidation of the structural and functional mechanism of action of the tetr family protein, cprb from S. coelicolor A3(2)
Analyse Elucidation of the structural and functional mechanism of action of the tetr… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PXI
- 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*CP*AP*TP*AP*CP*GP*GP*GP*AP*CP*GP*CP*CP*CP*CP*GP*TP*TP*TP*AP*T)- 3')…
- UniProt
- O66122
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 67% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cprb | protein | 194 | 70% helix, 0% strand | O66122 |
| B | Cprb | protein | 204 | 65% helix, 0% strand | O66122 |
| C | Cprb | protein | 200 | 66% helix, 1% strand | O66122 |
| D | Cprb | protein | 193 | 68% helix, 0% strand | O66122 |
| E | DNA (5'- D(*AP*CP*AP*TP*AP*CP*GP*GP*GP*AP*CP*GP*CP*CP*CP*CP*GP*TP*TP*TP*AP*T)- 3') | dna | 20 | — | — |
| F | DNA (5'- D(*AP*TP*AP*AP*AP*CP*GP*GP*GP*GP*CP*GP*TP*CP*CP*CP*GP*TP*AP*TP*GP*T)- 3') | dna | 22 | — | — |
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 901 | 0.83 | 0.85 | 110 | empty |
| 2 | 380 | 0.80 | 0.89 | 49 | empty |
| 3 | 602 | 0.79 | 0.85 | 87 | empty |
| 4 | 540 | 0.77 | 0.84 | 62 | empty |
| 5 | 73 | 0.72 | 0.96 | 19 | empty |
Interfaces
11 interfaces between chains.
- C–D · 1270 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1120 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 933 Ų buried · 93 hydrogen bonds · nucleic-nucleic
- C–F · 498 Ų buried · 6 hydrogen bonds · protein-nucleic
- C–E · 436 Ų buried · 6 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4PXI · Elucidation of the Structural and Functional Mechanism of Action of the TetR Family… · 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 4PXI · PDBe 4PXI · UniProt O66122
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