Research workbench
CDC48 hexamer (subunits a to E) with substrate bound to the central pore
Analyse CDC48 hexamer (subunits a to E) with substrate bound to the central pore in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OMB
- Type
- protein
- Length
- 2,797 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division control protein 48; Substrate of CDC48
- EC
- 3.6.4.6
- UniProt
- P25694
- Ligands
- ADP, BEF, MG
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 4 distinct chains · 43% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell division control protein 48 (EC 3.6.4.6) | protein | 556 | 44% helix, 9% strand | P25694 |
| B, C, D | Cell division control protein 48 (EC 3.6.4.6) | protein | 561 | 43% helix, 9% strand | P25694 |
| E | Cell division control protein 48 (EC 3.6.4.6) | protein | 536 | 44% helix, 9% strand | P25694 |
| G | Substrate of CDC48 | protein | 22 | 0% helix, 23% strand | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 10 copies · chains A, B, C, D, E
- BEF · Beryllium trifluoride ion · ligand · 8 copies · chains A, B, C, D, E
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E
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 | 902 | 0.81 | 0.84 | 91 | empty |
| 2 | 449 | 0.79 | 0.87 | 65 | ADP, BEF, MG |
| 3 | 754 | 0.78 | 0.82 | 88 | ADP, BEF, MG |
| 4 | 616 | 0.78 | 0.84 | 62 | ADP, MG, BEF |
| 5 | 656 | 0.76 | 0.82 | 74 | ADP, BEF, MG |
Interfaces
15 interfaces between chains.
- A–B · 5128 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 5126 Ų buried · 40 hydrogen bonds · protein-protein
- B–C · 5077 Ų buried · 37 hydrogen bonds · protein-protein
- D–E · 4857 Ų buried · 28 hydrogen bonds · protein-protein
- C–G · 487 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6OMB · Cdc48 Hexamer (Subunits A to E) with substrate bound to the central pore · the same entry in another collection · chain G against G, TM-score 1.00
- P25694 · AlphaFold monomer V2.0 prediction for cell division control protein 48 (P25694) · a predicted model of the same protein · chain E against A, TM-score 0.77
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 P25694
- Elsewhere: RCSB PDB 6OMB · PDBe 6OMB · UniProt P25694
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