MolNFT v1 · #191529 · protein
Activated spinach rubisco complexed with 2-carboxyarabinitol bisphosphate
8RUC · Ribulose-1,5-bisphosphate CARBOXYLASE/OXYGENASE: “Activated spinach rubisco complexed with 2-carboxyarabinitol bisphosphate”. X-ray diffraction, 2 ligands (CAP, MG), 20 pockets (best druggability 0.77). MolNFT v1 #191529 on…
- PDB
- 8RUC
- Type
- protein
- Length
- 2,360 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribulose-1,5-bisphosphate CARBOXYLASE/OXYGENASE
- EC
- 4.1.1.39
- UniProt
- P00875, P00870
- Ligands
- CAP, MG
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Ribulose-1,5-bisphosphate CARBOXYLASE/OXYGENASE (EC 4.1.1.39) | protein | 467 | 43% helix, 16% strand | P00875 |
| I, J, K, L | Ribulose-1,5-bisphosphate CARBOXYLASE/OXYGENASE (EC 4.1.1.39) | protein | 123 | 22% helix, 24% strand | P00870 |
Ligands and binding sites
- CAP · 2-carboxyarabinitol-1,5-diphosphate · ligand · 4 copies · chains A, C, E, G
- MG · Magnesium ion · metal · 4 copies · chains A, C, E, 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 | 101 | 0.77 | 0.98 | 27 | empty |
| 2 | 95 | 0.77 | 0.98 | 21 | empty |
| 3 | 95 | 0.77 | 0.98 | 21 | empty |
| 4 | 89 | 0.75 | 0.97 | 23 | empty |
| 5 | 246 | 0.65 | 0.83 | 44 | MG, CAP |
Interfaces
16 interfaces between chains.
- C–J · 1950 Ų buried · 27 hydrogen bonds · protein-protein
- A–I · 1950 Ų buried · 24 hydrogen bonds · protein-protein
- E–K · 1947 Ų buried · 24 hydrogen bonds · protein-protein
- G–L · 1945 Ų buried · 23 hydrogen bonds · protein-protein
- A–L · 979 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 8RUC · Activated spinach rubisco complexed with 2-carboxyarabinitol bisphosphate · the same entry in another collection · chain L against L, TM-score 1.00
- P00875 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase large chain… · a predicted model of the same protein · chain A against A, TM-score 0.99
- P00870 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase small subunit… · a predicted model of the same protein · chain I against A, TM-score 0.98
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 P00875
- Every structure of UniProt P00870
- Elsewhere: RCSB PDB 8RUC · PDBe 8RUC · UniProt P00875 · UniProt P00870
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.