Research workbench
Structural basis of cullin-2 ring E3 ligase regulation by the COP9 signalosome
Analyse Structural basis of cullin-2 ring E3 ligase regulation by the COP9 signalosome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6R7N
- Type
- protein
- Length
- 3,065 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- COP9 signalosome complex subunit 1; COP9 signalosome complex subunit 4; COP9 signalosome…
- UniProt
- Q13098, Q9BT78, Q99627, Q15370, Q15369, Q9UNS2, Q13617, P61201
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 10 distinct chains · 60% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | COP9 signalosome complex subunit 1 | protein | 419 | 67% helix, 2% strand | Q13098 |
| D | COP9 signalosome complex subunit 4 | protein | 406 | 69% helix, 3% strand | Q9BT78 |
| H | COP9 signalosome complex subunit 8 | protein | 169 | 64% helix, 4% strand | Q99627 |
| P | Elongin-B | protein | 104 | 14% helix, 8% strand | Q15370 |
| Q | Elongin-C | protein | 88 | 39% helix, 10% strand | Q15369 |
| R | RBX1 E3 ubiquitin-protein ligase | protein | 86 | 10% helix, 0% strand | — |
| C | COP9 signalosome complex subunit 3 | protein | 401 | 60% helix, 3% strand | Q9UNS2 |
| G | CSN7B_HUMAN | protein | 215 | 60% helix, 3% strand | — |
| O | Cullin-2 | protein | 734 | 61% helix, 1% strand | Q13617 |
| B | COP9 signalosome complex subunit 2 | protein | 443 | 66% helix, 3% strand | P61201 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains R, B
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 | 1065 | 0.87 | 0.88 | 108 | empty |
| 2 | 892 | 0.82 | 0.84 | 85 | empty |
| 3 | 875 | 0.82 | 0.84 | 82 | empty |
| 4 | 701 | 0.80 | 0.84 | 75 | empty |
| 5 | 236 | 0.75 | 0.89 | 45 | empty |
Interfaces
19 interfaces between chains.
- A–C · 2197 Ų buried · 39 hydrogen bonds · protein-protein
- R–O · 2067 Ų buried · 23 hydrogen bonds · protein-protein
- D–G · 1797 Ų buried · 67 hydrogen bonds · protein-protein
- P–Q · 1665 Ų buried · 12 hydrogen bonds · protein-protein
- O–B · 1654 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 6R7N · Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome · the same entry in another collection · chain B against B, TM-score 1.00
- Q9UNS2 · AlphaFold monomer V2.0 prediction for COP9 signalosome complex subunit 3 (Q9UNS2) · a predicted model of the same protein · chain C against A, TM-score 0.97
- Q13098 · AlphaFold monomer V2.0 prediction for COP9 signalosome complex subunit 1 (Q13098) · a predicted model of the same protein · chain A against A, TM-score 0.87
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 Q13098
- Every structure of UniProt Q9BT78
- Every structure of UniProt Q99627
- Every structure of UniProt Q15370
- Every structure of UniProt Q15369
- Every structure of UniProt Q9UNS2
- Every structure of UniProt Q13617
- Every structure of UniProt P61201
- Elsewhere: RCSB PDB 6R7N · PDBe 6R7N · UniProt Q13098 · UniProt Q9BT78 · UniProt Q99627 · UniProt Q15370 · UniProt Q15369 · UniProt Q9UNS2 · UniProt Q13617 · UniProt P61201
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