MolNFT v1 · #98630 · protein
Hexameric form II rubisco from rhodopseudomonas palustris, activated and complexed with sulfate and magnesium
4LF2 · Ribulose bisphosphate carboxylase: “Hexameric form II rubisco from rhodopseudomonas palustris, activated and complexed with sulfate and magnesium”. X-ray diffraction, 3 ligands (MG, SO4, CO3), 20 pockets (best druggability 0.84).…
- PDB
- 4LF2
- Type
- protein
- Length
- 2,731 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
- MG, SO4, CO3
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 457 | 45% helix, 18% strand | Q6N0W9 |
| B, C | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 453 | 44% helix, 18% strand | Q6N0W9 |
| E | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 455 | 45% helix, 18% strand | Q6N0W9 |
| F | Ribulose bisphosphate carboxylase (EC 4.1.1.39) | protein | 456 | 45% helix, 18% strand | Q6N0W9 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D, E, F
- CO3 · Carbonate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1022 | 0.84 | 0.85 | 105 | empty |
| 2 | 1053 | 0.84 | 0.85 | 120 | empty |
| 3 | 1006 | 0.84 | 0.85 | 109 | empty |
| 4 | 136 | 0.82 | 0.99 | 36 | empty |
| 5 | 130 | 0.82 | 0.99 | 37 | empty |
Interfaces
12 interfaces between chains.
- C–D · 4330 Ų buried · 66 hydrogen bonds · protein-protein
- A–B · 4298 Ų buried · 70 hydrogen bonds · protein-protein
- E–F · 4285 Ų buried · 64 hydrogen bonds · protein-protein
- A–F · 1128 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 1120 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (carboxylation).
Compared structures
- 4LF2 · Hexameric Form II RuBisCO from Rhodopseudomonas palustris, activated and complexed with… · 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 E 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 4LF2 · PDBe 4LF2 · UniProt Q6N0W9
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