Research workbench
Crystal structure of the unactivated ribulose 1, 5-bisphosphate CARBOXYLASE(SLASH)OXYGENASE complexed with a transition state analog, 2-carboxy-D-arabinitol 1,5-bisphosphate
Analyse Crystal structure of the unactivated 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
- 1RLC
- Type
- protein
- Length
- 564 residues
- Chains
- 2
- 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
- P69249
- Ligands
- CAP
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Ribulose 1,5 bisphosphate CARBOXYLASE/OXYGENASE (large chain) (EC 4.1.1.39) | protein | 441 | 46% helix, 18% strand | — |
| S | Ribulose 1,5 bisphosphate CARBOXYLASE/OXYGENASE (small chain) (EC 4.1.1.39) | protein | 123 | 22% helix, 26% strand | P69249 |
Ligands and binding sites
- CAP · 2-carboxyarabinitol-1,5-diphosphate · ligand · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.72 | 0.97 | 19 | empty |
| 2 | 145 | 0.53 | 0.80 | 30 | empty |
| 3 | 188 | 0.46 | 0.74 | 30 | empty |
| 4 | 72 | 0.35 | 0.77 | 19 | empty |
| 5 | 66 | 0.28 | 0.74 | 20 | CAP |
Interfaces
1 interface between chains.
- L–S · 1882 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1RLC · Crystal structure of the unactivated ribulose 1, 5-bisphosphate… · the same entry in another collection · chain L against L, 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 0.99
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 P69249
- Elsewhere: RCSB PDB 1RLC · PDBe 1RLC · UniProt P69249
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