MolNFT v1 · #159891 · protein + DNA
Crystal structure of the xpb-BAX1-forked DNA ternary complex
6P4F · DNA-dependent ATPase xpbii: “Crystal structure of the xpb-BAX1-forked DNA ternary complex”. X-ray diffraction, 3 ligands (MG, CL, PO4), 20 pockets (best druggability 0.85). MolNFT v1 #159891 on GenesisL1: 3D structure, binding sites…
- PDB
- 6P4F
- Type
- protein + DNA
- Length
- 1,708 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-dependent ATPase xpbii; Endonuclease BAX1; DNA (5'…
- UniProt
- Q970I2, Q970I1
- Ligands
- MG, CL, PO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-dependent ATPase xpbii | protein | 435 | 36% helix, 17% strand | Q970I2 |
| B, D | Endonuclease BAX1 | protein | 373 | 37% helix, 18% strand | Q970I1 |
| C | DNA-dependent ATPase xpbii | protein | 436 | 37% helix, 18% strand | Q970I2 |
| E, G | DNA (5'- D(*TP*TP*GP*AP*CP*TP*CP*AP*AP*CP*AP*TP*CP*CP*TP*TP*TP*GP*CP*TP*AP*CP* AP*A)-3') | dna | 24 | — | — |
| F | DNA (5'- D(P*TP*GP*TP*AP*GP*GP*TP*TP*TP*CP*CP*AP*TP*GP*TP*TP*GP*AP*GP*TP*CP*A) -3') | dna | 22 | — | — |
| H | DNA (5'- D(P*TP*GP*TP*AP*GP*GP*TP*TP*TP*CP*CP*AP*TP*GP*TP*TP*GP*AP*GP*TP*CP*A) -3') | dna | 21 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 25 copies · chains A, E, F, B, C, D, H
- CL · Chloride ion · ion · 11 copies · chains A, B, F, G
- PO4 · Phosphate ion · ion · 3 copies · chains B, E, F, D, G, H
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 | 662 | 0.85 | 0.89 | 67 | MG, PO4 |
| 2 | 618 | 0.84 | 0.90 | 59 | empty |
| 3 | 617 | 0.80 | 0.86 | 52 | PO4 |
| 4 | 747 | 0.78 | 0.83 | 61 | empty |
| 5 | 468 | 0.77 | 0.86 | 56 | PO4, MG, CL |
Interfaces
20 interfaces between chains.
- C–D · 1263 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1222 Ų buried · 6 hydrogen bonds · protein-protein
- C–G · 1036 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–E · 1013 Ų buried · 14 hydrogen bonds · protein-nucleic
- C–H · 878 Ų buried · 15 hydrogen bonds · protein-nucleic
Compared structures
- 6P4F · Crystal structure of the XPB-Bax1-forked DNA ternary complex · 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 6P4F · PDBe 6P4F · UniProt Q970I2 · UniProt Q970I1
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