MolNFT v1 · #159948 · protein
The crystal structure of the xpb complex with BAX1 from archaeoglobus fulgidus at 3.0 ångström resolution
6P66 · DNA repair protein RAD25: “The crystal structure of the xpb complex with BAX1 from archaeoglobus fulgidus at 3.0 ångström resolution”. X-ray diffraction, 1 ligand (CL), 20 pockets (best druggability 0.78). MolNFT v1 #159948 on…
- 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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