MolNFT v1 · #77956 · protein
Crystal structure of the unactivated form of ribulose-1,5-bisphosphate CARBOXYLASE(SLASH)OXYGENASE from tobacco refined at 2.0-ångströms resolution
3RUB · Ribulose 1,5-bisphosphate CARBOXYLASE/OXYGENASE, form III: “Crystal structure of the unactivated form of ribulose-1,5-bisphosphate CARBOXYLASE(SLASH)OXYGENASE from…”. X-ray diffraction, 2 ligands (SO4, ASN), 7 pockets (best…
- PDB
- 3RUB
- 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, form III
- EC
- 4.1.1.39
- UniProt
- P00876, P69249
- Ligands
- SO4, ASN
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Ribulose 1,5-bisphosphate CARBOXYLASE/OXYGENASE, form III (EC 4.1.1.39) | protein | 441 | 46% helix, 18% strand | P00876 |
| S | Ribulose 1,5-bisphosphate CARBOXYLASE/OXYGENASE, form III (EC 4.1.1.39) | protein | 123 | 22% helix, 24% strand | P69249 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.73 | 0.98 | 19 | empty |
| 2 | 136 | 0.51 | 0.80 | 30 | empty |
| 3 | 186 | 0.47 | 0.76 | 27 | SO4 |
| 4 | 143 | 0.42 | 0.75 | 29 | empty |
| 5 | 53 | 0.36 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- L–S · 1883 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3RUB · Crystal structure of the unactivated form of 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
- P00876 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase large chain… · a predicted model of the same protein · chain L 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 3RUB · PDBe 3RUB · UniProt P00876 · UniProt P69249
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