MolNFT v1 · #10422 · protein
Crystal structure of spinach ribulose-1,5-bisphosphate CARBOXYLASE/OXYGENASE (rubisco) complexed with CO2, MG2+ and 2- carboxyarabinitol-1,5-bisphosphate
1IR1 · Large subunit of rubisco: “Crystal structure of spinach ribulose-1,5-bisphosphate CARBOXYLASE/OXYGENASE (rubisco) complexed with CO2…”. X-ray diffraction, 2 ligands (CAP, MG), 20 pockets (best druggability 0.76). MolNFT v1 #10422 on…
- PDB
- 1IR1
- Type
- protein
- Length
- 2,348 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Large subunit of rubisco; Small subunit of rubisco
- EC
- 4.1.1.39
- UniProt
- P00875, Q43832
- Ligands
- CAP, MG
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Large subunit of rubisco (EC 4.1.1.39) | protein | 464 | 44% helix, 17% strand | P00875 |
| S, T, U, V | Small subunit of rubisco (EC 4.1.1.39) | protein | 123 | 22% helix, 24% strand | Q43832 |
Ligands and binding sites
- CAP · 2-carboxyarabinitol-1,5-diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 89 | 0.76 | 0.98 | 21 | empty |
| 2 | 81 | 0.76 | 0.98 | 20 | empty |
| 3 | 85 | 0.76 | 0.98 | 28 | empty |
| 4 | 81 | 0.74 | 0.97 | 26 | empty |
| 5 | 418 | 0.65 | 0.78 | 62 | empty |
Interfaces
16 interfaces between chains.
- C–U · 1978 Ų buried · 22 hydrogen bonds · protein-protein
- A–S · 1957 Ų buried · 25 hydrogen bonds · protein-protein
- D–V · 1954 Ų buried · 27 hydrogen bonds · protein-protein
- B–T · 1946 Ų buried · 23 hydrogen bonds · protein-protein
- A–V · 977 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (carboxylation, nonstandard).
Compared structures
- 1IR1 · Crystal Structure of Spinach Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco)… · the same entry in another collection · chain V against V, TM-score 1.00
- P00875 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase large chain… · a predicted model of the same protein · chain A against A, TM-score 1.00
- Q43832 · 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
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 P00875
- Every structure of UniProt Q43832
- Elsewhere: RCSB PDB 1IR1 · PDBe 1IR1 · UniProt P00875 · UniProt Q43832
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