Research workbench
Activated spinach rubisco in complex with its substrate ribulose-1,5- bisphosphate and calcium
Analyse Activated spinach rubisco in complex with its substrate ribulose-1,5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RXO
- Type
- protein
- Length
- 2,312 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribulose bisphosphate CARBOXYLASE/OXYGENASE
- EC
- 4.1.1.39
- UniProt
- P00875, P00870
- Ligands
- RUB, CA
- Pockets
- 20 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, B, E, H | Ribulose bisphosphate CARBOXYLASE/OXYGENASE (EC 4.1.1.39) | protein | 455 | 44% helix, 17% strand | P00875 |
| S, C, F, I | Ribulose bisphosphate CARBOXYLASE/OXYGENASE (EC 4.1.1.39) | protein | 123 | 22% helix, 24% strand | P00870 |
Ligands and binding sites
- RUB · Ribulose-1,5-diphosphate · ligand · 4 copies · chains L, B, E, H
- CA · Calcium ion · metal · 4 copies · chains L, B, E, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 425 | 0.67 | 0.80 | 65 | empty |
| 2 | 331 | 0.64 | 0.80 | 40 | empty |
| 3 | 294 | 0.63 | 0.80 | 33 | empty |
| 4 | 266 | 0.62 | 0.80 | 33 | empty |
| 5 | 282 | 0.62 | 0.80 | 33 | empty |
Interfaces
16 interfaces between chains.
- B–C · 1900 Ų buried · 20 hydrogen bonds · protein-protein
- H–I · 1895 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1895 Ų buried · 20 hydrogen bonds · protein-protein
- L–S · 1889 Ų buried · 20 hydrogen bonds · protein-protein
- L–I · 1006 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 1RXO · Activated spinach rubisco in complex with its substrate ribulose-1,5-bisphosphate and… · the same entry in another collection · chain I against I, TM-score 1.00
- P00875 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase large chain… · a predicted model of the same protein · chain L against A, TM-score 0.98
- P00870 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase small subunit… · a predicted model of the same protein · chain S against A, TM-score 0.97
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 1RXO · PDBe 1RXO · UniProt P00875 · UniProt P00870
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