Research workbench
Hexameric form II rubisco from rhodopseudomonas palustris, activated and complexed with sulfate and magnesium
Analyse Hexameric form II rubisco from rhodopseudomonas palustris, activated and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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