MolNFT v1 · #20939 · protein
Crystal structure of the binary complex of ribulose-1,5-bisphosphate carboxylase and its product, 3-phospho-D-glycerate
1RUS · Rubisco (ribulose-1,5-bisphosphate CARBOXYLASE(SLASH)…: “Crystal structure of the binary complex of ribulose-1,5-bisphosphate carboxylase and its product…”. X-ray diffraction, 1 ligand (3PG), 7 pockets (best druggability 0.83).…
- PDB
- 1RUS
- Type
- protein
- Length
- 872 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rubisco (ribulose-1,5-bisphosphate CARBOXYLASE(SLASH) oxygenase)
- EC
- 4.1.1.39
- UniProt
- P04718
- Ligands
- 3PG
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rubisco (ribulose-1,5-bisphosphate CARBOXYLASE(SLASH) oxygenase) (EC 4.1.1.39) | protein | 437 | 37% helix, 16% strand | P04718 |
| B | Rubisco (ribulose-1,5-bisphosphate CARBOXYLASE(SLASH) oxygenase) (EC 4.1.1.39) | protein | 435 | 40% helix, 19% strand | P04718 |
Ligands and binding sites
- 3PG · 3-phosphoglyceric acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 240 | 0.83 | 0.96 | 46 | empty |
| 2 | 546 | 0.63 | 0.75 | 67 | 3PG |
| 3 | 476 | 0.63 | 0.76 | 59 | 3PG |
| 4 | 85 | 0.37 | 0.76 | 21 | empty |
| 5 | 69 | 0.35 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 3027 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 1RUS · Crystal structure of the binary complex of ribulose-1,5-bisphosphate carboxylase and its… · the same entry in another collection · chain A against A, TM-score 1.00
- P04718 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase (P04718) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P04718
- Elsewhere: RCSB PDB 1RUS · PDBe 1RUS · UniProt P04718
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