Research workbench
Structural basis for cooperative binding of ribbon-helix-helix repressor omega to mutated direct DNA heptad repeats
Analyse Structural basis for cooperative binding of ribbon-helix-helix repressor omega… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CAX
- Type
- protein + DNA
- Length
- 273 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*G)- 3'…
- UniProt
- Q57468
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 7 distinct chains · 66% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Orf omega | protein | 53 | 70% helix, 13% strand | Q57468 |
| B | Orf omega | protein | 50 | 66% helix, 14% strand | Q57468 |
| D | Orf omega | protein | 47 | 62% helix, 15% strand | Q57468 |
| G | 5'-D(*GP*AP*AP*TP*CP*AP*CP*AP*AP*AP *TP*CP*AP*CP*AP*AP*G)- 3' | dna | 17 | — | — |
| H | 5'-D(*TP*TP*GP*TP*GP*AP*TP*TP*TP*GP *TP*GP*AP*TP*TP*CP*G)- 3' | dna | 17 | — | — |
| U | 5'-D(*GP*AP*AP*TP*CP*AP*CP*AP*AP*GP *TP*CP*AP*CP*AP*AP*GP*C)-3' | dna | 18 | — | — |
| Y | 5'-D(*CP*TP*TP*GP*TP*GP*AP*CP*TP*TP *GP*TP*GP*AP*TP*TP*CP*G)-3' | dna | 18 | — | — |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 364 | 0.60 | 0.78 | 50 | empty |
| 2 | 63 | 0.30 | 0.75 | 13 | empty |
| 3 | 70 | 0.28 | 0.73 | 13 | empty |
Interfaces
18 interfaces between chains.
- C–D · 1968 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1867 Ų buried · 23 hydrogen bonds · protein-protein
- U–Y · 808 Ų buried · 67 hydrogen bonds · nucleic-nucleic
- G–H · 720 Ų buried · 59 hydrogen bonds · nucleic-nucleic
- A–Y · 297 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 2CAX · Structural basis for cooperative binding of ribbon-helix-helix repressor omega to mutated… · 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 2CAX · PDBe 2CAX · UniProt Q57468
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