Research workbench
CDC48-NPL4 complex processing poly-ubiquitinated substrate in the presence of ADP-befx, state 2
Analyse CDC48-NPL4 complex processing poly-ubiquitinated substrate in the presence of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OAB
- Type
- protein
- Length
- 2,537 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division control protein 48; POLY(ALANINE) substrate
- EC
- 3.6.4.6
- UniProt
- P25694
- Ligands
- ADP, BEF
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 6 distinct chains · 33% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Cell division control protein 48 (EC 3.6.4.6) | protein | 537 | 30% helix, 9% strand | P25694 |
| E | Cell division control protein 48 (EC 3.6.4.6) | protein | 442 | 35% helix, 10% strand | P25694 |
| B | Cell division control protein 48 (EC 3.6.4.6) | protein | 509 | 36% helix, 9% strand | P25694 |
| C | Cell division control protein 48 (EC 3.6.4.6) | protein | 532 | 31% helix, 10% strand | P25694 |
| A | Cell division control protein 48 (EC 3.6.4.6) | protein | 493 | 37% helix, 9% strand | P25694 |
| H | POLY(ALANINE) substrate | protein | 24 | 0% helix, 13% strand | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 10 copies · chains D, E, B, C, A
- BEF · Beryllium trifluoride ion · ligand · 8 copies · chains D, E, B, A, C
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 | 0.82 | 0.83 | 98 | BEF, ADP |
| 2 | 876 | 0.81 | 0.83 | 94 | ADP, BEF |
| 3 | 716 | 0.80 | 0.84 | 93 | ADP, BEF |
| 4 | 370 | 0.80 | 0.89 | 54 | BEF |
| 5 | 536 | 0.80 | 0.86 | 81 | empty |
Interfaces
14 interfaces between chains.
- D–C · 4647 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 4263 Ų buried · 40 hydrogen bonds · protein-protein
- D–E · 4132 Ų buried · 43 hydrogen bonds · protein-protein
- B–A · 3681 Ų buried · 32 hydrogen bonds · protein-protein
- B–H · 436 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 21 covalent (covalent ligand).
Compared structures
- 6OAB · 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
- 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 0.81
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 6OAB · PDBe 6OAB · UniProt P25694
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.