Research workbench
Solid-state phase transition in the crystal structure of ribulose 1,5- biphosphate CARBOXYLASE(SLASH)OXYGENASE
Analyse Solid-state phase transition in the crystal structure of ribulose 1,5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RLD
- Type
- protein
- Length
- 1,128 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribulose 1,5 bisphosphate CARBOXYLASE/OXYGENASE (large chain); Ribulose 1,5 bisphosphate…
- EC
- 4.1.1.39
- UniProt
- P00876, P69249
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribulose 1,5 bisphosphate CARBOXYLASE/OXYGENASE (large chain) (EC 4.1.1.39) | protein | 441 | 43% helix, 19% strand | P00876 |
| S, T | Ribulose 1,5 bisphosphate CARBOXYLASE/OXYGENASE (small chain) (EC 4.1.1.39) | protein | 123 | 23% helix, 24% strand | P69249 |
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 940 | 0.77 | 0.80 | 77 | empty |
| 2 | 838 | 0.74 | 0.79 | 75 | empty |
| 3 | 75 | 0.74 | 0.98 | 22 | empty |
| 4 | 69 | 0.73 | 0.98 | 20 | empty |
| 5 | 53 | 0.73 | 0.99 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3220 Ų buried · 64 hydrogen bonds · protein-protein
- B–T · 1853 Ų buried · 27 hydrogen bonds · protein-protein
- A–S · 1851 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 1RLD · Solid-state phase transition in the crystal structure of ribulose 1,5-biphosphate… · the same entry in another collection · chain A against A, 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 0.98
- P00876 · 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 P00876
- Every structure of UniProt P69249
- Elsewhere: RCSB PDB 1RLD · PDBe 1RLD · UniProt P00876 · UniProt P69249
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.