MolNFT v1 · #88638 · protein
Crystal structure of the COP9 signalosome
4D10 · COP9 signalosome complex subunit 1: “Crystal structure of the COP9 signalosome”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.78). MolNFT v1 #88638 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4D10
- Type
- protein
- Length
- 4,997 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- COP9 signalosome complex subunit 1; COP9 signalosome complex subunit 2; COP9 signalosome…
- EC
- 3.4.-.-
- UniProt
- Q13098, P61201, Q9UNS2, Q9BT78, Q92905, Q7L5N1, Q9UBW8, Q99627
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 9 distinct chains · 64% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, I | COP9 signalosome complex subunit 1 | protein | 419 | 71% helix, 3% strand | Q13098 |
| B, J | COP9 signalosome complex subunit 2 | protein | 403 | 68% helix, 3% strand | P61201 |
| C, K | COP9 signalosome complex subunit 3 | protein | 401 | 61% helix, 3% strand | Q9UNS2 |
| D | COP9 signalosome complex subunit 4 | protein | 406 | 73% helix, 4% strand | Q9BT78 |
| E, M | COP9 signalosome complex subunit 5 (EC 3.4.-.-) | protein | 298 | 52% helix, 17% strand | Q92905 |
| F, N | COP9 signalosome complex subunit 6 | protein | 281 | 47% helix, 23% strand | Q7L5N1 |
| G, O | COP9 signalosome complex subunit 7A | protein | 208 | 62% helix, 8% strand | Q9UBW8 |
| H, P | COP9 signalosome complex subunit 8 | protein | 173 | 68% helix, 6% strand | Q99627 |
| L | COP9 signalosome complex subunit 4 | protein | 225 | 70% helix, 7% strand | Q9BT78 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains E, M
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 | 861 | 0.78 | 0.81 | 88 | empty |
| 2 | 1045 | 0.77 | 0.79 | 103 | empty |
| 3 | 604 | 0.76 | 0.82 | 81 | empty |
| 4 | 614 | 0.72 | 0.80 | 63 | empty |
| 5 | 161 | 0.71 | 0.90 | 31 | empty |
Interfaces
48 interfaces between chains.
- E–F · 4012 Ų buried · 17 hydrogen bonds · protein-protein
- M–N · 4008 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 2278 Ų buried · 22 hydrogen bonds · protein-protein
- I–K · 2249 Ų buried · 26 hydrogen bonds · protein-protein
- L–N · 2044 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4D10 · Crystal structure of the COP9 signalosome · the same entry in another collection · chain K against K, TM-score 1.00
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 P61201
- Every structure of UniProt Q9UNS2
- Every structure of UniProt Q9BT78
- Every structure of UniProt Q92905
- Every structure of UniProt Q7L5N1
- Every structure of UniProt Q9UBW8
- Every structure of UniProt Q99627
- Elsewhere: RCSB PDB 4D10 · PDBe 4D10 · UniProt Q13098 · UniProt P61201 · UniProt Q9UNS2 · UniProt Q9BT78 · UniProt Q92905 · UniProt Q7L5N1 · UniProt Q9UBW8 · UniProt Q99627
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