MolNFT v1 · #150624 · protein
Heterotetrameric katanin P60:P80 complex
6GZC · Katanin P80 WD40 repeat-containing subunit B1: “Heterotetrameric katanin P60:P80 complex”. X-ray diffraction, 6 pockets (best druggability 0.84). MolNFT v1 #150624 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6GZC
- Type
- protein
- Length
- 480 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Katanin P80 WD40 repeat-containing subunit B1; Katanin P60 ATPase-containing subunit A1
- EC
- 3.6.4.3
- UniProt
- Q8BG40, Q9WV86
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 85% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Katanin P80 WD40 repeat-containing subunit B1 | protein | 165 | 87% helix, 0% strand | Q8BG40 |
| B | Katanin P60 ATPase-containing subunit A1 (EC 3.6.4.3) | protein | 77 | 83% helix, 0% strand | Q9WV86 |
| D | Katanin P60 ATPase-containing subunit A1 (EC 3.6.4.3) | protein | 76 | 88% helix, 0% strand | Q9WV86 |
| C | Katanin P80 WD40 repeat-containing subunit B1 | protein | 162 | 84% helix, 0% strand | Q8BG40 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1121 | 0.84 | 0.84 | 83 | PEG, EDO |
| 2 | 182 | 0.44 | 0.74 | 23 | empty |
| 3 | 129 | 0.41 | 0.75 | 19 | empty |
| 4 | 108 | 0.39 | 0.75 | 20 | empty |
| 5 | 109 | 0.38 | 0.75 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1618 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1434 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1413 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 89 Ų buried · 0 hydrogen bonds · protein-protein
- D–C · 86 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6GZC · heterotetrameric katanin p60:p80 complex · the same entry in another collection · chain C against C, TM-score 1.00
- Q9WV86 · AlphaFold monomer V2.0 prediction for katanin P60 ATPase-containing subunit A1 (Q9WV86) · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q8BG40 · AlphaFold monomer V2.0 prediction for katanin P80 WD40 repeat- containing subunit B1… · a predicted model of the same protein · chain A against A, TM-score 0.64
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 Q8BG40
- Every structure of UniProt Q9WV86
- Elsewhere: RCSB PDB 6GZC · PDBe 6GZC · UniProt Q8BG40 · UniProt Q9WV86
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