Research workbench
Crystal structure of DDB1 in complex with the H-box motif of WDR42A
Analyse Crystal structure of DDB1 in complex with the H-box motif of WDR42A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3I8E
- Type
- protein
- Length
- 2,254 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA damage-binding protein 1; Wd repeat-containing protein 42A
- UniProt
- Q16531, Q5TAQ9
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA damage-binding protein 1 | protein | 1114 | 4% helix, 43% strand | Q16531 |
| C, D | Wd repeat-containing protein 42A | protein | 13 | 0% helix, 0% strand | Q5TAQ9 |
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 815 | 0.80 | 0.83 | 81 | empty |
| 2 | 1052 | 0.80 | 0.81 | 83 | empty |
| 3 | 795 | 0.79 | 0.82 | 78 | empty |
| 4 | 930 | 0.79 | 0.81 | 75 | empty |
| 5 | 877 | 0.78 | 0.81 | 64 | empty |
Interfaces
3 interfaces between chains.
- B–D · 798 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 760 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 160 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3I8E · Crystal Structure of DDB1 in Complex with the H-Box Motif of WDR42A · 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 A against A, TM-score 0.88
- Q5TAQ9 · AlphaFold monomer V2.0 prediction for DDB1- and CUL4-associated factor 8 (Q5TAQ9) · a predicted model of the same protein · chain D against A, TM-score 0.52
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 Q5TAQ9
- Elsewhere: RCSB PDB 3I8E · PDBe 3I8E · UniProt Q16531 · UniProt Q5TAQ9
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