MolNFT v1 · #121280 · protein
Structure function studies of R. palustris rubisco (R. PALUSTRIS/R. rubrum chimera)
5HQM · Ribulose bisphosphate carboxylase (R. PALUSTRIS/R. rubrum…: “Structure function studies of R. palustris rubisco (R. PALUSTRIS/R. rubrum chimera)”. X-ray diffraction, 3 ligands (CAP, MG, K), 6 pockets (best druggability 0.82). MolNFT…
- PDB
- 5HQM
- Type
- protein
- Length
- 913 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribulose bisphosphate carboxylase (R. PALUSTRIS/R. rubrum CHIMERA),RIBULOSE bisphosphate…
- EC
- 4.1.1.39
- UniProt
- Q6N0W9, P04718
- Ligands
- CAP, MG, K
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribulose bisphosphate carboxylase (R. PALUSTRIS/R. rubrum CHIMERA),RIBULOSE bisphosphate carboxylase (EC 4.1.1.39) | protein | 459 | 44% helix, 18% strand | Q6N0W9, P04718 |
| B | Ribulose bisphosphate carboxylase (R. PALUSTRIS/R. rubrum CHIMERA),RIBULOSE bisphosphate carboxylase (EC 4.1.1.39) | protein | 454 | 44% helix, 18% strand | Q6N0W9, P04718 |
Ligands and binding sites
- CAP · 2-carboxyarabinitol-1,5-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 153 | 0.82 | 0.98 | 38 | empty |
| 2 | 363 | 0.74 | 0.85 | 75 | CAP, MG |
| 3 | 419 | 0.71 | 0.82 | 76 | CAP |
| 4 | 72 | 0.54 | 0.86 | 21 | empty |
| 5 | 100 | 0.41 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 4258 Ų buried · 64 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 5HQM · Structure function studies of R. palustris RubisCO (R. palustris/R. rubrum chimera) · the same entry in another collection · chain A against A, 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
- P04718 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase (P04718) · a predicted model of the same protein · chain B against A, TM-score 0.99
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
- Every structure of UniProt P04718
- Elsewhere: RCSB PDB 5HQM · PDBe 5HQM · UniProt Q6N0W9 · UniProt P04718
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