Research workbench
Spinach rubisco in complex with 2-carboxyarabinitol 2 bisphosphate and calcium.
Analyse Spinach rubisco in complex with 2-carboxyarabinitol 2 bisphosphate and calcium. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UPP
- Type
- protein
- Length
- 2,360 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase small…
- EC
- 4.1.1.39
- UniProt
- P00875, Q43832
- Ligands
- CAP, CA
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 467 | 44% helix, 17% strand | P00875 |
| I, J, K, L | Ribulose bisphosphate carboxylase small chain (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, C, E, G
- CA · Calcium ion · metal · 4 copies · chains A, C, E, G
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 | 104 | 0.78 | 0.98 | 25 | empty |
| 2 | 103 | 0.77 | 0.98 | 27 | empty |
| 3 | 100 | 0.77 | 0.97 | 20 | empty |
| 4 | 96 | 0.76 | 0.97 | 24 | empty |
| 5 | 399 | 0.64 | 0.79 | 58 | empty |
Interfaces
16 interfaces between chains.
- G–L · 1914 Ų buried · 26 hydrogen bonds · protein-protein
- C–J · 1914 Ų buried · 25 hydrogen bonds · protein-protein
- E–K · 1914 Ų buried · 24 hydrogen bonds · protein-protein
- A–I · 1912 Ų buried · 24 hydrogen bonds · protein-protein
- G–K · 993 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 1UPP · SPINACH RUBISCO IN COMPLEX WITH 2-CARBOXYARABINITOL 2 BISPHOSPHATE and Calcium. · the same entry in another collection · chain L against L, 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 0.99
- Q43832 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase small subunit… · a predicted model of the same protein · chain I 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 1UPP · PDBe 1UPP · UniProt P00875 · UniProt Q43832
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