Research workbench
Crystal structure of DDB1 in complex with DET1- and DDB1-associated protein 1 (DDA1)
Analyse Crystal structure of DDB1 in complex with DET1- and DDB1-associated protein 1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DSZ
- Type
- protein
- Length
- 2,217 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA damage-binding protein 1; DET1- and DDB1-associated protein 1
- UniProt
- Q16531, Q9BW61
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA damage-binding protein 1 | protein | 1107 | 3% helix, 46% strand | Q16531 |
| B | DNA damage-binding protein 1 | protein | 1072 | 3% helix, 46% strand | Q16531 |
| C, D | DET1- and DDB1-associated protein 1 | protein | 19 | 0% helix, 0% strand | Q9BW61 |
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1098 | 0.78 | 0.80 | 86 | empty |
| 2 | 1156 | 0.78 | 0.80 | 83 | empty |
| 3 | 1092 | 0.77 | 0.79 | 80 | empty |
| 4 | 1036 | 0.77 | 0.79 | 88 | empty |
| 5 | 1097 | 0.77 | 0.79 | 86 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1185 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1164 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 549 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6DSZ · Crystal structure of DDB1 in complex with DET1- and DDB1-associated protein 1 (DDA1) · the same entry in another collection · chain D against D, TM-score 1.00
- Q16531 · AlphaFold monomer V2.0 prediction for DNA damage-binding protein 1 (Q16531) · a predicted model of the same protein · chain B against A, TM-score 0.90
- Q9BW61 · AlphaFold monomer V2.0 prediction for DET1- and DDB1-associated protein 1 (Q9BW61) · a predicted model of the same protein · chain C against A, TM-score 0.26
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 Q16531
- Every structure of UniProt Q9BW61
- Elsewhere: RCSB PDB 6DSZ · PDBe 6DSZ · UniProt Q16531 · UniProt Q9BW61
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