Research workbench
Crystal structure of DDB1 in complex with the H-box motif of WDR21A
Analyse Crystal structure of DDB1 in complex with the H-box motif of WDR21A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3I8C
- Type
- protein
- Length
- 1,127 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA damage-binding protein 1; Wd repeat-containing protein 21A
- UniProt
- Q16531, Q8WV16
- Pockets
- 19 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA damage-binding protein 1 | protein | 1114 | 5% helix, 42% strand | Q16531 |
| B | Wd repeat-containing protein 21A | protein | 13 | 69% helix, 0% strand | Q8WV16 |
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1139 | 0.80 | 0.81 | 78 | empty |
| 2 | 596 | 0.77 | 0.83 | 51 | empty |
| 3 | 798 | 0.75 | 0.79 | 66 | empty |
| 4 | 295 | 0.70 | 0.84 | 39 | empty |
| 5 | 56 | 0.70 | 0.97 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 640 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3I8C · Crystal Structure of DDB1 in Complex with the H-Box Motif of WDR21A · the same entry in another collection · chain A against A, 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
- Q8WV16 · AlphaFold monomer V2.0 prediction for DDB1- and CUL4-associated factor 4 (Q8WV16) · a predicted model of the same protein · chain B against A, TM-score 0.51
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 Q8WV16
- Elsewhere: RCSB PDB 3I8C · PDBe 3I8C · UniProt Q16531 · UniProt Q8WV16
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