MolNFT v1 · #121063 · protein
Structure function studies of R. palustris rubisco (A47V-M331A mutant)
5HK4 · Ribulose bisphosphate carboxylase: “Structure function studies of R. palustris rubisco (A47V-M331A mutant)”. X-ray diffraction, 2 ligands (CAP, MG), 20 pockets (best druggability 0.84). MolNFT v1 #121063 on GenesisL1: 3D structure…
- PDB
- 5HK4
- Type
- protein
- Length
- 2,733 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 0.84
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 457 | 44% helix, 18% strand | Q6N0W9 |
| B, C, E, F | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 455 | 44% helix, 18% strand | Q6N0W9 |
| D | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 456 | 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 895 | 0.84 | 0.86 | 86 | empty |
| 2 | 935 | 0.82 | 0.84 | 95 | empty |
| 3 | 147 | 0.82 | 0.98 | 36 | empty |
| 4 | 139 | 0.82 | 0.98 | 34 | empty |
| 5 | 133 | 0.81 | 0.97 | 37 | empty |
Interfaces
12 interfaces between chains.
- E–F · 4229 Ų buried · 62 hydrogen bonds · protein-protein
- C–D · 4225 Ų buried · 66 hydrogen bonds · protein-protein
- A–B · 4196 Ų buried · 65 hydrogen bonds · protein-protein
- D–E · 1113 Ų buried · 12 hydrogen bonds · protein-protein
- A–F · 1100 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (carboxylation).
Compared structures
- 5HK4 · Structure function studies of R. palustris RubisCO (A47V-M331A mutant) · 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 5HK4 · PDBe 5HK4 · UniProt Q6N0W9
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