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The crystal structure of the xpb complex with BAX1 from archaeoglobus fulgidus at 3.0 ångström resolution
Analyse The crystal structure of the xpb complex with BAX1 from archaeoglobus fulgidus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P66
- Type
- protein
- Length
- 1,837 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA repair protein RAD25; DNA endonuclease BAX1
- UniProt
- O29889, O29890
- Ligands
- CL
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA repair protein RAD25 | protein | 443 | 41% helix, 20% strand | O29889 |
| B, D | DNA endonuclease BAX1 | protein | 467 | 38% helix, 15% strand | O29890 |
| C | DNA repair protein RAD25 | protein | 460 | 36% helix, 23% strand | O29889 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.78 | 0.80 | 95 | empty |
| 2 | 819 | 0.77 | 0.81 | 81 | empty |
| 3 | 768 | 0.76 | 0.81 | 78 | empty |
| 4 | 858 | 0.75 | 0.79 | 100 | empty |
| 5 | 910 | 0.69 | 0.74 | 87 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1850 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 1621 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1509 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 552 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6P66 · The crystal structure of the XPB complex with Bax1 from Archaeoglobus fulgidus at 3.0… · 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
- Every structure of UniProt O29889
- Every structure of UniProt O29890
- Elsewhere: RCSB PDB 6P66 · PDBe 6P66 · UniProt O29889 · UniProt O29890
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