MolNFT v1 · #62523 · protein
Structure of the HSDDB1-HSDDB2 complex
3EI4 · DNA damage-binding protein 1: “Structure of the HSDDB1-HSDDB2 complex”. X-ray diffraction, 20 pockets (best druggability 0.87). MolNFT v1 #62523 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3EI4
- Type
- protein
- Length
- 4,524 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA damage-binding protein 1; DNA damage-binding protein 2
- UniProt
- Q16531, Q92466
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | DNA damage-binding protein 1 | protein | 1140 | 5% helix, 47% strand | Q16531 |
| B, D, F | DNA damage-binding protein 2 | protein | 368 | 8% helix, 36% strand | Q92466 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1029 | 0.87 | 0.88 | 105 | empty |
| 2 | 622 | 0.84 | 0.89 | 71 | empty |
| 3 | 1137 | 0.83 | 0.84 | 90 | empty |
| 4 | 394 | 0.81 | 0.89 | 53 | empty |
| 5 | 1118 | 0.80 | 0.82 | 72 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2612 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 2587 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 2537 Ų buried · 17 hydrogen bonds · protein-protein
- B–F · 277 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 181 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3EI4 · Structure of the hsDDB1-hsDDB2 complex · the same entry in another collection · chain F against F, TM-score 1.00
- Q92466 · AlphaFold monomer V2.0 prediction for DNA damage-binding protein 2 (Q92466) · a predicted model of the same protein · chain F against A, TM-score 0.97
- Q16531 · AlphaFold monomer V2.0 prediction for DNA damage-binding protein 1 (Q16531) · a predicted model of the same protein · chain E against A, TM-score 0.86
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 Q92466
- Elsewhere: RCSB PDB 3EI4 · PDBe 3EI4 · UniProt Q16531 · UniProt Q92466
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