Research workbench
Structure of HSDDB1-DRDDB2 bound to a 16 bp cpd-duplex (pyrimidine at D-1 position) at 3.6 a resolution (cpd 3)
Analyse Structure of HSDDB1-DRDDB2 bound to a 16 bp cpd-duplex (pyrimidine at D-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4A0A
- Type
- protein + DNA
- Length
- 1,166 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
- Ligands
- CA
- Pockets
- 19 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA damage-binding protein 1 | protein | 780 | 6% helix, 49% strand | Q16531 |
| B | DNA damage-binding protein 2 | protein | 355 | 8% helix, 40% strand | Q2YDS1 |
| C | 5'-D(*GP*GP*TP*GP*AP*AP*AP*(TTD)P*AP*GP*CP*AP*GP*DGP)-3' | dna | 15 | — | — |
| D | 5'-D(*CP*CP*TP*GP*CP*TP*CP*CP*TP*TP*TP*CP*AP*CP*CP*C)-3' | dna | 16 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 933 | 0.86 | 0.87 | 99 | empty |
| 2 | 1179 | 0.83 | 0.84 | 101 | empty |
| 3 | 545 | 0.78 | 0.84 | 53 | empty |
| 4 | 434 | 0.67 | 0.79 | 39 | empty |
| 5 | 522 | 0.66 | 0.77 | 50 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2287 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 695 Ų buried · 14 hydrogen bonds · protein-nucleic
- C–D · 637 Ų buried · 43 hydrogen bonds · nucleic-nucleic
- B–D · 458 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4A0A · Structure of hsDDB1-drDDB2 bound to a 16 bp CPD-duplex (pyrimidine at D-1 position) at… · 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 0.99
- 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 0.98
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 4A0A · PDBe 4A0A · UniProt Q16531 · UniProt Q2YDS1
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