MolNFT v1 · #159900 · protein
Complex of xpb helicase with BAX1 endonuclease from sulfurisphaera tokodaii at 3.15 ångströms resolution
6P4O · DNA-dependent ATPase xpbii: “Complex of xpb helicase with BAX1 endonuclease from sulfurisphaera tokodaii at 3.15 ångströms resolution”. X-ray diffraction, 1 ligand (CL), 20 pockets (best druggability 0.83). MolNFT v1 #159900 on…
- PDB
- 6P4O
- Type
- protein
- Length
- 2,753 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-dependent ATPase xpbii; Endonuclease BAX1
- UniProt
- Q970I2, Q970I1
- Ligands
- CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-dependent ATPase xpbii | protein | 442 | 43% helix, 20% strand | Q970I2 |
| B | Endonuclease BAX1 | protein | 479 | 40% helix, 17% strand | Q970I1 |
| C | DNA-dependent ATPase xpbii | protein | 437 | 43% helix, 20% strand | Q970I2 |
| D | Endonuclease BAX1 | protein | 477 | 39% helix, 16% strand | Q970I1 |
| E | DNA-dependent ATPase xpbii | protein | 437 | 43% helix, 20% strand | Q970I2 |
| F | Endonuclease BAX1 | protein | 481 | 40% helix, 16% strand | Q970I1 |
Ligands and binding sites
- CL · Chloride ion · ion · 5 copies · chains A, C, F
- GOL · Glycerol · additive · 2 copies · chains A, E, C
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 962 | 0.83 | 0.84 | 99 | empty |
| 2 | 1164 | 0.81 | 0.82 | 106 | empty |
| 3 | 740 | 0.76 | 0.81 | 69 | empty |
| 4 | 604 | 0.75 | 0.81 | 71 | empty |
| 5 | 561 | 0.72 | 0.81 | 67 | empty |
Interfaces
12 interfaces between chains.
- A–B · 1479 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1443 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1326 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 638 Ų buried · 5 hydrogen bonds · protein-protein
- B–F · 632 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6P4O · Complex of XPB helicase with Bax1 endonuclease from Sulfurisphaera tokodaii at 3.15… · 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 Q970I2
- Every structure of UniProt Q970I1
- Elsewhere: RCSB PDB 6P4O · PDBe 6P4O · UniProt Q970I2 · UniProt Q970I1
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