Research workbench
Activated spinach rubisco complexed with 2-carboxyarabinitol 2 bisphosphat and CA2+.
Analyse Activated spinach rubisco complexed with 2-carboxyarabinitol 2 bisphosphat and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UPM
- Type
- protein
- Length
- 4,720 residues
- Chains
- 16
- 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 0.85
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, E, H, K, L, O, R, V | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 467 | 43% helix, 17% strand | P00875 |
| C, F, I, M, P, S, T, W | 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 · 8 copies · chains B, L, E, H, K, O, R, V
- CA · Calcium ion · metal · 8 copies · chains B, L, E, H, K, O, R, V
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 | 1033 | 0.85 | 0.86 | 124 | empty |
| 2 | 1118 | 0.84 | 0.86 | 125 | empty |
| 3 | 1054 | 0.84 | 0.86 | 120 | empty |
| 4 | 177 | 0.83 | 0.98 | 46 | CA, CAP |
| 5 | 171 | 0.82 | 0.98 | 45 | CA, CAP |
Interfaces
48 interfaces between chains.
- E–H · 4868 Ų buried · 80 hydrogen bonds · protein-protein
- B–L · 4859 Ų buried · 81 hydrogen bonds · protein-protein
- R–V · 4859 Ų buried · 80 hydrogen bonds · protein-protein
- K–O · 4852 Ų buried · 79 hydrogen bonds · protein-protein
- V–W · 1955 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (carboxylation).
Compared structures
- 1UPM · Activated spinach rubisco complexed with 2-carboxyarabinitol 2 bisphosphat and CA2+. · the same entry in another collection · chain W against W, TM-score 1.00
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 1UPM · PDBe 1UPM · UniProt P00875 · UniProt Q43832
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