Research workbench
Complex of xpb helicase with BAX1 endonuclease from sulfurisphaera tokodaii at 3.15 ångströms resolution
Analyse Complex of xpb helicase with BAX1 endonuclease from sulfurisphaera tokodaii at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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