Research workbench
Structure of HSDDB1-DRDDB2 bound to a 16 bp abasic site containing DNA-duplex
Analyse Structure of HSDDB1-DRDDB2 bound to a 16 bp abasic site containing DNA-duplex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EI2
- Type
- protein + DNA
- Length
- 1,488 residues
- Chains
- 4
- 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
- 18 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA damage-binding protein 1 | protein | 1103 | 6% helix, 54% strand | Q16531 |
| B | DNA damage-binding protein 2 | protein | 355 | 7% helix, 45% strand | Q2YDS1 |
| G | 5'-D(*DAP*DAP*DAP*DTP*DGP*DAP*DAP*DTP*(3DR) P*DAP*DAP*DGP*DCP*DAP*DGP*DG)-3' | dna | 15 | — | — |
| H | 5'- D(*DCP*DCP*DTP*DGP*DCP*DTP*DTP*DTP*DAP*DTP*DTP*DCP*DAP*DTP* DTP*DT)-3' | dna | 15 | — | — |
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
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 912 | 0.87 | 0.88 | 111 | empty |
| 2 | 1182 | 0.84 | 0.85 | 106 | empty |
| 3 | 1187 | 0.84 | 0.85 | 112 | empty |
| 4 | 390 | 0.76 | 0.85 | 41 | empty |
| 5 | 845 | 0.76 | 0.79 | 65 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2104 Ų buried · 19 hydrogen bonds · protein-protein
- B–G · 620 Ų buried · 9 hydrogen bonds · protein-nucleic
- G–H · 572 Ų buried · 54 hydrogen bonds · nucleic-nucleic
- B–H · 460 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3EI2 · Structure of hsDDB1-drDDB2 bound to a 16 bp abasic site containing DNA-duplex · 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 0.90
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 3EI2 · PDBe 3EI2 · UniProt Q16531 · UniProt Q2YDS1
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