MolNFT v1 · #32354 · protein + DNA
Structural basis for cooperative binding of ribbon-helix-helix omega repressor to direct DNA heptad repeats
2BNW · Orf omega: “Structural basis for cooperative binding of ribbon-helix-helix omega repressor to direct DNA heptad repeats”. X-ray diffraction, 4 pockets (best druggability 0.60). MolNFT v1 #32354 on GenesisL1: 3D structure, binding…
- PDB
- 2BNW
- Type
- protein + DNA
- Length
- 272 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orf omega; 5'-D(*GP*AP*AP*TP*CP*AP*CP*AP*AP*AP *TP*CP*AP*CP*AP*AP*GP*C)-3'…
- UniProt
- Q57468
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 5 distinct chains · 68% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orf omega | protein | 49 | 67% helix, 14% strand | Q57468 |
| B, C | Orf omega | protein | 53 | 70% helix, 13% strand | Q57468 |
| D | Orf omega | protein | 47 | 68% helix, 15% strand | Q57468 |
| E, G | 5'-D(*GP*AP*AP*TP*CP*AP*CP*AP*AP*AP *TP*CP*AP*CP*AP*AP*GP*C)-3' | dna | 17 | — | — |
| F, H | 5'-D(*CP*TP*TP*GP*TP*GP*AP*TP*TP*TP *GP*TP*GP*AP*TP*TP*CP*G)-3' | dna | 18 | — | — |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 310 | 0.60 | 0.79 | 44 | empty |
| 2 | 66 | 0.29 | 0.74 | 13 | empty |
| 3 | 62 | 0.29 | 0.75 | 12 | empty |
| 4 | 51 | 0.26 | 0.74 | 11 | empty |
Interfaces
18 interfaces between chains.
- C–D · 1974 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1884 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 820 Ų buried · 61 hydrogen bonds · nucleic-nucleic
- G–H · 782 Ų buried · 69 hydrogen bonds · nucleic-nucleic
- B–F · 302 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 2BNW · Structural basis for cooperative binding of Ribbon-Helix-Helix Omega repressor to direct… · 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 Q57468
- Elsewhere: RCSB PDB 2BNW · PDBe 2BNW · UniProt Q57468
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