Research workbench
Structure of the HSDDB1-DRDDB2 complex
Analyse Structure of the HSDDB1-DRDDB2 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EI3
- Type
- protein
- Length
- 1,460 residues
- Chains
- 2
- 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, Q2YDS1
- Pockets
- 14 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA damage-binding protein 1 | protein | 1105 | 6% helix, 53% strand | Q16531 |
| B | DNA damage-binding protein 2 | protein | 355 | 8% helix, 47% strand | Q2YDS1 |
Ligands and binding sites
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 787 | 0.86 | 0.89 | 109 | empty |
| 2 | 608 | 0.84 | 0.89 | 79 | empty |
| 3 | 795 | 0.78 | 0.82 | 75 | empty |
| 4 | 628 | 0.76 | 0.82 | 49 | empty |
| 5 | 123 | 0.65 | 0.88 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1990 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3EI3 · Structure of the hsDDB1-drDDB2 complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q2YDS1 · AlphaFold monomer V2.0 prediction for DNA damage-binding protein 2 (Q2YDS1) · a predicted model of the same protein · chain B against A, TM-score 0.99
- 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 0.94
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 Q2YDS1
- Elsewhere: RCSB PDB 3EI3 · PDBe 3EI3 · UniProt Q16531 · UniProt Q2YDS1
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