Research workbench
Structure function studies of R. palustris RubisCO (M331A mutant; CABP-bound)
Analyse Structure function studies of R. palustris RubisCO (M331A 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
- 5HAO
- Type
- protein
- Length
- 2,730 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.182
- Source
- Rhodopseudomonas palustris
- Molecule
- Ribulose bisphosphate carboxylase
- EC
- 4.1.1.39
- UniProt
- Q6N0W9
- Ligands
- CAP, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.182 · 1 distinct chain · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, 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 · sugar · 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 | 628 | 0.82 | 0.87 | 72 | empty |
| 2 | 795 | 0.82 | 0.85 | 80 | empty |
| 3 | 137 | 0.82 | 0.98 | 37 | empty |
| 4 | 132 | 0.81 | 0.98 | 37 | empty |
| 5 | 567 | 0.81 | 0.87 | 69 | empty |
Interfaces
12 interfaces between chains.
- C–D · 4184 Ų buried · 65 hydrogen bonds · protein-protein
- E–F · 4182 Ų buried · 67 hydrogen bonds · protein-protein
- A–B · 4167 Ų buried · 65 hydrogen bonds · protein-protein
- D–E · 1142 Ų buried · 14 hydrogen bonds · protein-protein
- A–F · 1126 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (carboxylation).
Compared structures
- 5HAO · Structure function studies of R. palustris rubisco (M331A mutant; cabp-bound) · the same entry in another collection · chain C against C, TM-score 1.00
- Q6N0W9 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase (Q6N0W9) · a predicted model of the same protein · chain A 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 5HAO · PDBe 5HAO · UniProt Q6N0W9
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