Research workbench
Xpb helicase in a complex with truncated BAX1 from sulfurisphaera tokodaii at 2.96 ångström resolution
Analyse Xpb helicase in a complex with truncated BAX1 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
- 6P4W
- Type
- protein
- Length
- 1,617 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-dependent ATPase xpbii; Endonuclease BAX1
- UniProt
- Q970I2, Q970I1
- Ligands
- MG, CL, PO4
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | DNA-dependent ATPase xpbii | protein | 435 | 42% helix, 21% strand | Q970I2 |
| B | Endonuclease BAX1 | protein | 374 | 41% helix, 21% strand | Q970I1 |
| D | Endonuclease BAX1 | protein | 373 | 41% helix, 21% strand | Q970I1 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, C
- CL · Chloride ion · ion · 18 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 2 copies · chains A, C
- GOL · Glycerol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 856 | 0.73 | 0.77 | 83 | empty |
| 2 | 582 | 0.65 | 0.76 | 70 | CL |
| 3 | 82 | 0.60 | 0.88 | 18 | empty |
| 4 | 212 | 0.58 | 0.80 | 32 | empty |
| 5 | 100 | 0.57 | 0.86 | 25 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1705 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1659 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 716 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6P4W · XPB helicase in a complex with truncated Bax1 from Sulfurisphaera tokodaii at 2.96… · 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 6P4W · PDBe 6P4W · UniProt Q970I2 · UniProt Q970I1
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