Research workbench
Crystal structure of the winged-helix domain of cockayne syndrome group B protein in complex with ubiquitin
Analyse Crystal structure of the winged-helix domain of cockayne syndrome group B… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6A6I
- Type
- protein
- Length
- 660 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Excision repair cross-complementing rodent repair deficiency, complementation group 6…
- UniProt
- Q59FF6, P0CG47
- Ligands
- CL
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Excision repair cross-complementing rodent repair deficiency, complementation group 6 variant | protein | 94 | 48% helix, 16% strand | Q59FF6 |
| B | Polyubiquitin-B | protein | 74 | 24% helix, 34% strand | P0CG47 |
| D | Polyubiquitin-B | protein | 76 | 24% helix, 33% strand | P0CG47 |
| F, H | Polyubiquitin-B | protein | 74 | 24% helix, 34% strand | P0CG47 |
| G | Excision repair cross-complementing rodent repair deficiency, complementation group 6 variant | protein | 80 | 53% helix, 19% strand | Q59FF6 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 584 | 0.82 | 0.87 | 70 | empty |
| 2 | 165 | 0.66 | 0.87 | 34 | empty |
| 3 | 340 | 0.63 | 0.79 | 41 | empty |
| 4 | 81 | 0.54 | 0.85 | 22 | empty |
| 5 | 60 | 0.52 | 0.87 | 13 | empty |
Interfaces
18 interfaces between chains.
- A–C · 923 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 740 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 730 Ų buried · 15 hydrogen bonds · protein-protein
- G–H · 690 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 689 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 isopeptide (disulfide, isopeptide).
Compared structures
- 6A6I · Crystal structure of the winged-helix domain of Cockayne syndrome group B protein in… · 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 Q59FF6
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 6A6I · PDBe 6A6I · UniProt Q59FF6 · UniProt P0CG47
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