Research workbench
Crystal structure of activated ribulose-1,5-bisphosphate carboxylase complexed with its substrate, ribulose-1,5-bisphosphate
Analyse Crystal structure of activated ribulose-1,5-bisphosphate carboxylase complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 9RUB
- Type
- protein
- Length
- 917 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribulose-1,5-bisphosphate carboxylase
- EC
- 4.1.1.39
- UniProt
- P04718
- Ligands
- RUB, MG
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribulose-1,5-bisphosphate carboxylase (EC 4.1.1.39) | protein | 459 | 33% helix, 16% strand | P04718 |
| B | Ribulose-1,5-bisphosphate carboxylase (EC 4.1.1.39) | protein | 458 | 37% helix, 17% strand | P04718 |
Ligands and binding sites
- RUB · Ribulose-1,5-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- FMT · Formic acid · additive · 2 copies · chains A, B
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 | 228 | 0.83 | 0.96 | 42 | empty |
| 2 | 1135 | 0.78 | 0.80 | 74 | RUB, MG, FMT |
| 3 | 944 | 0.72 | 0.76 | 99 | RUB, MG |
| 4 | 118 | 0.44 | 0.77 | 22 | empty |
| 5 | 81 | 0.39 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 3528 Ų buried · 43 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct).
Compared structures
- 9RUB · Crystal structure of activated ribulose-1,5-bisphosphate carboxylase complexed with its… · 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 9RUB · PDBe 9RUB · UniProt P04718
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.