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Structure of HSDDB1-DRDDB2 bound to a 13 bp cpd-duplex (purine at D-1 position) at 3.0 a resolution (cpd 1)
Analyse Structure of HSDDB1-DRDDB2 bound to a 13 bp cpd-duplex (purine at D-1 position)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4A08
- Type
- protein + DNA
- Length
- 1,464 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
- 17 · best druggability 0.86
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 | 1088 | 5% helix, 53% strand | Q16531 |
| B | DNA damage-binding protein 2 | protein | 353 | 7% helix, 46% strand | Q2YDS1 |
| G | 5'-D(*AP*CP*GP*CP*GP*AP*(TTD)P*GP*CP*GP*CP*CP*C)-3' | dna | 10 | — | — |
| H | 5'-D(*TP*GP*GP*GP*CP*GP*CP*CP*CP*TP*CP*GP*CP*G)-3' | dna | 13 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains B, H, G
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 912 | 0.86 | 0.87 | 93 | empty |
| 2 | 883 | 0.85 | 0.87 | 95 | MES |
| 3 | 1004 | 0.84 | 0.85 | 74 | empty |
| 4 | 592 | 0.78 | 0.84 | 52 | empty |
| 5 | 146 | 0.78 | 0.95 | 25 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2176 Ų buried · 20 hydrogen bonds · protein-protein
- B–G · 660 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–H · 643 Ų buried · 11 hydrogen bonds · protein-nucleic
- G–H · 477 Ų buried · 48 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4A08 · Structure of hsDDB1-drDDB2 bound to a 13 bp CPD-duplex (purine at D-1 position) at 3.0 A… · 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 0.84
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 4A08 · PDBe 4A08 · UniProt Q16531 · UniProt Q2YDS1
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