Research workbench
Structure function studies of R. palustris rubisco (A47V-M331A mutant; cabp-bound; no expression tag)
Analyse Structure function studies of R. palustris rubisco (A47V-M331A mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HQL
- Type
- protein
- Length
- 2,735 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 · 4 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 456 | 44% helix, 18% strand | Q6N0W9 |
| B, E | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 457 | 44% helix, 18% strand | Q6N0W9 |
| D | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 455 | 44% helix, 18% strand | Q6N0W9 |
| F | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 454 | 43% helix, 18% strand | Q6N0W9 |
Ligands and binding sites
- CAP · 2-carboxyarabinitol-1,5-diphosphate · ligand · 6 copies · chains A, B, C, E, D, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, E, D, 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 894 | 0.83 | 0.85 | 98 | empty |
| 2 | 947 | 0.83 | 0.84 | 101 | empty |
| 3 | 887 | 0.82 | 0.84 | 82 | empty |
| 4 | 142 | 0.82 | 0.98 | 39 | empty |
| 5 | 138 | 0.81 | 0.98 | 39 | empty |
Interfaces
12 interfaces between chains.
- C–E · 4163 Ų buried · 62 hydrogen bonds · protein-protein
- D–F · 4163 Ų buried · 60 hydrogen bonds · protein-protein
- A–B · 4149 Ų buried · 61 hydrogen bonds · protein-protein
- B–D · 1128 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1120 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (carboxylation).
Compared structures
- 5HQL · Structure function studies of R. palustris RubisCO (A47V-M331A mutant; CABP-bound; no… · 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 5HQL · PDBe 5HQL · UniProt Q6N0W9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.