MolNFT v1 · #121057 · protein
Structure function studies of R. palustris rubisco (I165T mutant; cabp-bound)
5HJY · Ribulose bisphosphate carboxylase: “Structure function studies of R. palustris rubisco (I165T mutant; cabp-bound)”. X-ray diffraction, 3 ligands (CAP, MG, CL), 20 pockets (best druggability 0.83). MolNFT v1 #121057 on GenesisL1: 3D…
- PDB
- 5HJY
- Type
- protein
- Length
- 2,729 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, CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, F | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 455 | 44% helix, 18% strand | Q6N0W9 |
| B | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 456 | 45% helix, 18% strand | Q6N0W9 |
| C | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 453 | 45% 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
- CL · Chloride ion · ion · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 758 | 0.83 | 0.87 | 86 | empty |
| 2 | 1010 | 0.83 | 0.84 | 108 | empty |
| 3 | 629 | 0.82 | 0.87 | 82 | empty |
| 4 | 134 | 0.82 | 0.98 | 38 | empty |
| 5 | 128 | 0.81 | 0.98 | 36 | empty |
Interfaces
12 interfaces between chains.
- E–F · 4330 Ų buried · 67 hydrogen bonds · protein-protein
- C–D · 4291 Ų buried · 67 hydrogen bonds · protein-protein
- A–B · 4274 Ų buried · 64 hydrogen bonds · protein-protein
- B–C · 1143 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 1130 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (carboxylation).
Compared structures
- 5HJY · Structure function studies of R. palustris RubisCO (I165T 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 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 5HJY · PDBe 5HJY · UniProt Q6N0W9
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