Research workbench
Structure function studies of R. palustris rubisco (A47V mutant; cabp- bound)
Analyse Structure function studies of R. palustris rubisco (A47V mutant; cabp- bound) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HJX
- Type
- protein
- Length
- 2,732 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribulose bisphosphate carboxylase
- EC
- 4.1.1.39
- UniProt
- Q6N0W9
- Ligands
- CAP, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 456 | 44% helix, 18% strand | Q6N0W9 |
| B, C, D, F | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 455 | 44% helix, 18% strand | Q6N0W9 |
Ligands and binding sites
- CAP · 2-carboxyarabinitol-1,5-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 894 | 0.83 | 0.85 | 93 | empty |
| 2 | 937 | 0.82 | 0.84 | 113 | empty |
| 3 | 123 | 0.81 | 0.99 | 36 | empty |
| 4 | 132 | 0.80 | 0.97 | 34 | empty |
| 5 | 716 | 0.80 | 0.84 | 79 | empty |
Interfaces
12 interfaces between chains.
- C–D · 4276 Ų buried · 65 hydrogen bonds · protein-protein
- A–B · 4269 Ų buried · 65 hydrogen bonds · protein-protein
- E–F · 4267 Ų buried · 65 hydrogen bonds · protein-protein
- D–E · 1122 Ų buried · 14 hydrogen bonds · protein-protein
- A–F · 1120 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (carboxylation).
Compared structures
- 5HJX · Structure function studies of R. palustris RubisCO (A47V mutant; CABP-bound) · the same entry in another collection · chain F against F, TM-score 1.00
- Q6N0W9 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase (Q6N0W9) · a predicted model of the same protein · chain B against A, 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 Q6N0W9
- Elsewhere: RCSB PDB 5HJX · PDBe 5HJX · UniProt Q6N0W9
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