Research workbench
CDC48-NPL4 complex processing poly-ubiquitinated substrate in the presence of ATP
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
- 6OA9
- Type
- protein
- Length
- 3,718 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division control protein 48; Ubiquitin; Nuclear protein localization protein 4
- EC
- 3.6.4.6
- UniProt
- P25694, P0CH08, P33755
- Ligands
- ATP, ADP, ZN
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 9 distinct chains · 33% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell division control protein 48 (EC 3.6.4.6) | protein | 547 | 36% helix, 9% strand | P25694 |
| B | Cell division control protein 48 (EC 3.6.4.6) | protein | 493 | 36% helix, 9% strand | P25694 |
| C | Cell division control protein 48 (EC 3.6.4.6) | protein | 492 | 34% helix, 9% strand | P25694 |
| D | Cell division control protein 48 (EC 3.6.4.6) | protein | 489 | 34% helix, 10% strand | P25694 |
| E | Cell division control protein 48 (EC 3.6.4.6) | protein | 496 | 34% helix, 10% strand | P25694 |
| F | Cell division control protein 48 (EC 3.6.4.6) | protein | 533 | 32% helix, 9% strand | P25694 |
| K | Ubiquitin | protein | 48 | 17% helix, 2% strand | P0CH08 |
| H, J | Ubiquitin | protein | 76 | 16% helix, 33% strand | P0CH08 |
| G | Nuclear protein localization protein 4 | protein | 468 | 28% helix, 14% strand | P33755 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 9 copies · chains A, B, C, D, E, F
- ADP · Adenosine-5'-diphosphate · ligand · chains E
- ZN · Zinc ion · metal · 2 copies · chains G
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 | 0.86 | 0.87 | 132 | ATP |
| 2 | 843 | 0.85 | 0.87 | 95 | empty |
| 3 | 368 | 0.85 | 0.93 | 57 | empty |
| 4 | 393 | 0.85 | 0.93 | 65 | empty |
| 5 | 930 | 0.83 | 0.85 | 109 | ATP |
Interfaces
24 interfaces between chains.
- B–C · 3656 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 2967 Ų buried · 23 hydrogen bonds · protein-protein
- D–E · 2644 Ų buried · 25 hydrogen bonds · protein-protein
- A–F · 2518 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2448 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 covalent (covalent ligand).
Compared structures
- 6OA9 · Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP · the same entry in another collection · chain J against J, 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 B against A, TM-score 0.91
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 P0CH08
- Every structure of UniProt P33755
- Elsewhere: RCSB PDB 6OA9 · PDBe 6OA9 · UniProt P25694 · UniProt P0CH08 · UniProt P33755
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