Research workbench
Unactivated rubisco with magnesium and carbon dioxide bound
Analyse Unactivated rubisco with magnesium and carbon dioxide bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4F0K
- Type
- protein
- Length
- 586 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase small…
- EC
- 4.1.1.39
- UniProt
- P23755, P23756
- Ligands
- MG, CO2, CL
- Pockets
- 9 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 448 | 42% helix, 17% strand | P23755 |
| B | Ribulose bisphosphate carboxylase small chain (EC 4.1.1.39) | protein | 138 | 24% helix, 30% strand | P23756 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
- CO2 · Carbon dioxide · ion · chains A
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 493 | 0.64 | 0.77 | 47 | empty |
| 2 | 185 | 0.53 | 0.79 | 30 | empty |
| 3 | 253 | 0.53 | 0.76 | 31 | empty |
| 4 | 129 | 0.44 | 0.77 | 23 | MG, CO2 |
| 5 | 97 | 0.43 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1579 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 4F0K · UNACTIVATED RUBISCO with MAGNESIUM AND CARBON DIOXIDE BOUND · the same entry in another collection · chain A against A, TM-score 1.00
- P23756 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase small subunit… · a predicted model of the same protein · chain B against A, TM-score 0.99
- P23755 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase large chain… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P23755
- Every structure of UniProt P23756
- Elsewhere: RCSB PDB 4F0K · PDBe 4F0K · UniProt P23755 · UniProt P23756
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