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Structure of HSDDB1-DRDDB2 bound to a 14 bp 6-4 photoproduct containing DNA-duplex
Analyse Structure of HSDDB1-DRDDB2 bound to a 14 bp 6-4 photoproduct containing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EI1
- 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
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 51% 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 | 7% helix, 45% strand | Q2YDS1 |
| G | 5'-D(*DAP*DCP*DGP*DCP*DGP*DAP*(64T)P*(5PY) P*DGP*DCP*DGP*DCP*DCP*DC)-3' | dna | 14 | — | — |
| H | 5'- D(*DTP*DGP*DGP*DGP*DCP*DGP*DCP*DAP*DAP*DTP*DCP*DGP*DCP*DG)- 3' | dna | 14 | — | — |
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
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 539 | 0.85 | 0.91 | 68 | empty |
| 2 | 1066 | 0.84 | 0.85 | 105 | empty |
| 3 | 355 | 0.79 | 0.89 | 59 | empty |
| 4 | 607 | 0.79 | 0.84 | 48 | empty |
| 5 | 559 | 0.76 | 0.83 | 54 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2002 Ų buried · 16 hydrogen bonds · protein-protein
- B–G · 608 Ų buried · 7 hydrogen bonds · protein-nucleic
- G–H · 580 Ų buried · 50 hydrogen bonds · nucleic-nucleic
- B–H · 411 Ų buried · 6 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3EI1 · Structure of hsDDB1-drDDB2 bound to a 14 bp 6-4 photoproduct 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 3EI1 · PDBe 3EI1 · UniProt Q16531 · UniProt Q2YDS1
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