Research workbench
Crystallographic refinement and structure of ribulose-1,5-bisphosphate carboxylase from rhodospirillum rubrum at 1.7 ångströms resolution
Analyse Crystallographic refinement and structure of 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
- 5RUB
- Type
- protein
- Length
- 869 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rubisco (ribulose-1,5-bisphosphate CARBOXYLASE(SLASH) oxygenase)
- EC
- 4.1.1.39
- UniProt
- P04718
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rubisco (ribulose-1,5-bisphosphate CARBOXYLASE(SLASH) oxygenase) (EC 4.1.1.39) | protein | 436 | 42% helix, 19% strand | P04718 |
| B | Rubisco (ribulose-1,5-bisphosphate CARBOXYLASE(SLASH) oxygenase) (EC 4.1.1.39) | protein | 433 | 42% helix, 18% strand | P04718 |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 241 | 0.84 | 0.96 | 43 | empty |
| 2 | 338 | 0.58 | 0.77 | 45 | empty |
| 3 | 287 | 0.55 | 0.76 | 47 | empty |
| 4 | 93 | 0.39 | 0.76 | 19 | empty |
| 5 | 82 | 0.37 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2933 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 5RUB · Crystallographic refinement and structure of ribulose-1,5-bisphosphate carboxylase from… · 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 0.97
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 5RUB · PDBe 5RUB · UniProt P04718
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