Research workbench
Crystal structure of the DDB1 bpb domain
Analyse Crystal structure of the DDB1 bpb domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2B5N
- Type
- protein
- Length
- 1,273 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Damage-specific DNA binding protein 1
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 0% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Damage-specific DNA binding protein 1 | protein | 312 | 0% helix, 55% strand | — |
| B | Damage-specific DNA binding protein 1 | protein | 321 | 0% helix, 55% strand | — |
| C | Damage-specific DNA binding protein 1 | protein | 320 | 0% helix, 54% strand | — |
| D | Damage-specific DNA binding protein 1 | protein | 320 | 0% helix, 54% strand | — |
Ligands and binding sites
- IPA · Isopropyl alcohol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 748 | 0.79 | 0.83 | 75 | empty |
| 2 | 676 | 0.78 | 0.83 | 57 | empty |
| 3 | 767 | 0.74 | 0.79 | 57 | empty |
| 4 | 820 | 0.73 | 0.78 | 58 | empty |
| 5 | 532 | 0.68 | 0.78 | 69 | empty |
Interfaces
3 interfaces between chains.
- A–C · 708 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 656 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 410 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2B5N · Crystal Structure of the DDB1 BPB Domain · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 2B5N · PDBe 2B5N
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