MolNFT v1 · #159438 · protein
CDC48 hexamer in a complex with substrate and SHP1(UBX domain)
6OPC · Cell division control protein 48: “CDC48 hexamer in a complex with substrate and SHP1(UBX domain)”. Electron microscopy, 3 ligands (ADP, BEF, MG), 20 pockets (best druggability 0.81). MolNFT v1 #159438 on GenesisL1: 3D structure…
- PDB
- 6OPC
- Type
- protein
- Length
- 4,477 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division control protein 48; Substrate bound to the central pore of the CDC48…
- EC
- 3.6.4.6
- UniProt
- P25694, P34223
- Ligands
- ADP, BEF, MG
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 6 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell division control protein 48 (EC 3.6.4.6) | protein | 733 | 38% helix, 15% strand | P25694 |
| B, C, D | Cell division control protein 48 (EC 3.6.4.6) | protein | 741 | 37% helix, 15% strand | P25694 |
| E | Cell division control protein 48 (EC 3.6.4.6) | protein | 716 | 38% helix, 15% strand | P25694 |
| F | Cell division control protein 48 (EC 3.6.4.6) | protein | 681 | 42% helix, 16% strand | P25694 |
| G | Substrate bound to the central pore of the CDC48 hexamer | protein | 22 | 0% helix, 23% strand | — |
| Z | Ubx domain-containing protein 1 | protein | 102 | 26% helix, 24% strand | P34223 |
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 | 1005 | 0.81 | 0.83 | 118 | empty |
| 2 | 987 | 0.81 | 0.83 | 120 | empty |
| 3 | 916 | 0.81 | 0.83 | 113 | empty |
| 4 | 1024 | 0.81 | 0.82 | 124 | empty |
| 5 | 1048 | 0.81 | 0.82 | 129 | empty |
Interfaces
19 interfaces between chains.
- A–B · 5129 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 5128 Ų buried · 41 hydrogen bonds · protein-protein
- B–C · 5087 Ų buried · 37 hydrogen bonds · protein-protein
- D–E · 4865 Ų buried · 27 hydrogen bonds · protein-protein
- A–F · 1207 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6OPC · Cdc48 Hexamer in a complex with substrate and Shp1(Ubx Domain) · the same entry in another collection · chain Z against Z, 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 A against A, TM-score 0.79
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
- Every structure of UniProt P34223
- Elsewhere: RCSB PDB 6OPC · PDBe 6OPC · UniProt P25694 · UniProt P34223
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