Research workbench
Crystal structure of unactivated tobacco rubisco with bound phosphate ions
Analyse Crystal structure of unactivated tobacco rubisco with bound phosphate ions in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EJ7
- Type
- protein
- Length
- 580 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rubisco (large subunit); Rubisco (small subunit)
- EC
- 4.1.1.39
- UniProt
- P00876, P69249
- Ligands
- PO4
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Rubisco (large subunit) (EC 4.1.1.39) | protein | 457 | 45% helix, 17% strand | P00876 |
| S | Rubisco (small subunit) (EC 4.1.1.39) | protein | 123 | 23% helix, 24% strand | P69249 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 3 copies · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.74 | 0.98 | 19 | empty |
| 2 | 247 | 0.51 | 0.76 | 35 | PO4 |
| 3 | 134 | 0.51 | 0.80 | 33 | empty |
| 4 | 125 | 0.43 | 0.77 | 27 | empty |
| 5 | 71 | 0.31 | 0.75 | 23 | PO4 |
Interfaces
1 interface between chains.
- L–S · 1884 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 1EJ7 · Crystal structure of unactivated tobacco rubisco with bound phosphate ions · the same entry in another collection · chain L against L, TM-score 1.00
- P69249 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase small subunit… · a predicted model of the same protein · chain S against A, TM-score 0.99
- P00876 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase large chain… · a predicted model of the same protein · chain L against A, TM-score 0.96
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 P00876
- Every structure of UniProt P69249
- Elsewhere: RCSB PDB 1EJ7 · PDBe 1EJ7 · UniProt P00876 · UniProt P69249
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