Research workbench
Spinach rubisco in complex with the inhibitor 2-carboxyarabinitol-1,5- diphosphate
Analyse Spinach rubisco in complex with the inhibitor 2-carboxyarabinitol-1,5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RBO
- Type
- protein
- Length
- 2,360 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
- CAP
- 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 |
|---|---|---|---|---|---|
| L, B, E, H | Ribulose bisphosphate CARBOXYLASE/OXYGENASE (EC 4.1.1.39) | protein | 467 | 44% helix, 16% 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
- CAP · 2-carboxyarabinitol-1,5-diphosphate · ligand · 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.77 | 0.98 | 26 | empty |
| 2 | 92 | 0.76 | 0.98 | 24 | empty |
| 3 | 93 | 0.75 | 0.97 | 22 | empty |
| 4 | 82 | 0.75 | 0.98 | 21 | empty |
| 5 | 257 | 0.65 | 0.82 | 42 | CAP |
Interfaces
16 interfaces between chains.
- L–S · 1952 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 1951 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1950 Ų buried · 26 hydrogen bonds · protein-protein
- H–I · 1944 Ų buried · 26 hydrogen bonds · protein-protein
- F–H · 979 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 1RBO · Spinach rubisco in complex with the inhibitor 2-carboxyarabinitol-1,5-diphosphate · 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 0.99
- 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 0.98
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 1RBO · PDBe 1RBO · UniProt P00875 · UniProt P00870
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