Research workbench
Crystal structure of the ternary complex of ribulose-1,5-bisphosphate carboxylase, MG(II), and activator CO2 at 2.3-ångströms resolution
Analyse Crystal structure of the ternary complex of ribulose-1,5-bisphosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2RUS
- Type
- protein
- Length
- 881 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rubisco (ribulose-1,5-bisphosphate CARBOXYLASE(SLASH) oxygenase)
- EC
- 4.1.1.39
- UniProt
- P04718
- Ligands
- FOR, MG
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rubisco (ribulose-1,5-bisphosphate CARBOXYLASE(SLASH) oxygenase) (EC 4.1.1.39) | protein | 437 | 41% helix, 19% strand | P04718 |
| B | Rubisco (ribulose-1,5-bisphosphate CARBOXYLASE(SLASH) oxygenase) (EC 4.1.1.39) | protein | 444 | 41% helix, 18% strand | P04718 |
Ligands and binding sites
- FOR · Formyl group · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 265 | 0.84 | 0.96 | 44 | empty |
| 2 | 994 | 0.76 | 0.78 | 91 | MG, FOR |
| 3 | 50 | 0.71 | 0.99 | 21 | empty |
| 4 | 397 | 0.60 | 0.76 | 57 | MG, FOR |
| 5 | 103 | 0.40 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 3122 Ų buried · 49 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2RUS · Crystal structure of the ternary complex of ribulose-1,5-bisphosphate carboxylase… · the same entry in another collection · chain A against A, TM-score 1.00
- P04718 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase (P04718) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P04718
- Elsewhere: RCSB PDB 2RUS · PDBe 2RUS · UniProt P04718
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.