Research workbench
Crystal structure of archaeal rubisco (ribulose 1,5-bisphosphate CARBOXYLASE/OXYGENASE)
Analyse Crystal structure of archaeal rubisco (ribulose 1,5-bisphosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GEH
- Type
- protein
- Length
- 2,135 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribulose-1,5-bisphosphate CARBOXYLASE/OXYGENASE
- EC
- 4.1.1.39
- UniProt
- O93627
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Ribulose-1,5-bisphosphate CARBOXYLASE/OXYGENASE (EC 4.1.1.39) | protein | 427 | 41% helix, 16% strand | O93627 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.52 | 0.86 | 20 | empty |
| 2 | 143 | 0.47 | 0.77 | 25 | empty |
| 3 | 127 | 0.45 | 0.78 | 24 | empty |
| 4 | 128 | 0.44 | 0.77 | 24 | empty |
| 5 | 116 | 0.44 | 0.78 | 24 | empty |
Interfaces
5 interfaces between chains.
- B–C · 261 Ų buried · 3 hydrogen bonds · protein-protein
- D–E · 253 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 253 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 251 Ų buried · 2 hydrogen bonds · protein-protein
- A–E · 251 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1GEH · Crystal structure of archaeal rubisco (ribulose 1,5-bisphosphate CARBOXYLASE/OXYGENASE) · the same entry in another collection · chain A against A, TM-score 1.00
- O93627 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase (O93627) · 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 O93627
- Elsewhere: RCSB PDB 1GEH · PDBe 1GEH · UniProt O93627
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.