MolNFT v1 · #158968 · protein
CDC48-NPL4 complex processing poly-ubiquitinated substrate in the presence of ADP-befx, state 1
6OAA · Cell division control protein 48: “CDC48-NPL4 complex processing poly-ubiquitinated substrate in the presence of ADP-befx, state 1”. Electron microscopy, 2 ligands (ADP, BEF), 20 pockets (best druggability 0.82). MolNFT v1 #158968…
- PDB
- 6OAA
- Type
- protein
- Length
- 2,494 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division control protein 48; Nuclear protein localization protein 4; Ubiquitin
- EC
- 3.6.4.6
- UniProt
- P25694, P33755, P0CH08
- Ligands
- ADP, BEF
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 6 distinct chains · 32% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Cell division control protein 48 (EC 3.6.4.6) | protein | 509 | 36% helix, 7% strand | P25694 |
| C | Cell division control protein 48 (EC 3.6.4.6) | protein | 532 | 32% helix, 9% strand | P25694 |
| D | Cell division control protein 48 (EC 3.6.4.6) | protein | 537 | 33% helix, 8% strand | P25694 |
| E | Cell division control protein 48 (EC 3.6.4.6) | protein | 442 | 34% helix, 10% strand | P25694 |
| G | Nuclear protein localization protein 4 | protein | 426 | 26% helix, 15% strand | P33755 |
| H | Ubiquitin | protein | 48 | 10% helix, 4% strand | P0CH08 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 8 copies · chains B, C, D, E
- BEF · Beryllium trifluoride ion · ligand · 6 copies · chains 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 | 652 | 0.82 | 0.87 | 67 | BEF, ADP |
| 2 | 742 | 0.79 | 0.83 | 58 | ADP |
| 3 | 540 | 0.79 | 0.85 | 64 | ADP |
| 4 | 153 | 0.78 | 0.94 | 39 | empty |
| 5 | 649 | 0.78 | 0.83 | 75 | ADP, BEF |
Interfaces
15 interfaces between chains.
- C–D · 4774 Ų buried · 49 hydrogen bonds · protein-protein
- B–C · 4332 Ų buried · 44 hydrogen bonds · protein-protein
- D–E · 4087 Ų buried · 49 hydrogen bonds · protein-protein
- G–H · 1714 Ų buried · 17 hydrogen bonds · protein-protein
- D–G · 642 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 covalent (covalent ligand).
Compared structures
- 6OAA · Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ADP-BeFx… · the same entry in another collection · chain H against H, TM-score 1.00
- P33755 · AlphaFold monomer V2.0 prediction for nuclear protein localization protein 4 (P33755) · a predicted model of the same protein · chain G against A, TM-score 0.94
- 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 0.79
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 P33755
- Every structure of UniProt P0CH08
- Elsewhere: RCSB PDB 6OAA · PDBe 6OAA · UniProt P25694 · UniProt P33755 · UniProt P0CH08
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