Research workbench
Crystal structure of DDB1 in complex with the H-box motif of WDTC1
Analyse Crystal structure of DDB1 in complex with the H-box motif of WDTC1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3I7N
- 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 and tetratricopeptide repeats protein 1
- UniProt
- Q16531, Q8N5D0
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA damage-binding protein 1 | protein | 1114 | 5% helix, 44% strand | Q16531 |
| B | Wd and tetratricopeptide repeats protein 1 | protein | 13 | 69% helix, 0% strand | Q8N5D0 |
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1105 | 0.80 | 0.81 | 76 | empty |
| 2 | 571 | 0.77 | 0.83 | 44 | empty |
| 3 | 836 | 0.75 | 0.79 | 55 | empty |
| 4 | 455 | 0.71 | 0.81 | 43 | empty |
| 5 | 277 | 0.70 | 0.85 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 928 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3I7N · Crystal Structure of DDB1 in Complex with the H-Box Motif of WDTC1 · 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
- Q8N5D0 · AlphaFold monomer V2.0 prediction for wd and tetratricopeptide repeats protein 1 (Q8N5D0) · a predicted model of the same protein · chain B against A, TM-score 0.65
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 Q8N5D0
- Elsewhere: RCSB PDB 3I7N · PDBe 3I7N · UniProt Q16531 · UniProt Q8N5D0
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