Research workbench
Rubisco in the apo state
Analyse Rubisco in the apo state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JN4
- Type
- protein
- Length
- 4,520 residues
- Chains
- 16
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase small…
- EC
- 4.1.1.39
- UniProt
- A0A218N8A3, P08475
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 2 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 427 | 42% helix, 18% strand | A0A218N8A3 |
| B, D, F, H, J, L, N, P | Ribulose bisphosphate carboxylase small chain 2, chloroplastic (EC 4.1.1.39) | protein | 138 | 23% helix, 22% strand | P08475 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1012 | 0.85 | 0.86 | 115 | empty |
| 2 | 858 | 0.79 | 0.82 | 66 | empty |
| 3 | 869 | 0.78 | 0.81 | 66 | empty |
| 4 | 846 | 0.78 | 0.82 | 63 | empty |
| 5 | 966 | 0.75 | 0.78 | 83 | empty |
Interfaces
48 interfaces between chains.
- A–C · 2692 Ų buried · 48 hydrogen bonds · protein-protein
- I–K · 2677 Ų buried · 47 hydrogen bonds · protein-protein
- E–G · 2674 Ų buried · 47 hydrogen bonds · protein-protein
- M–O · 2651 Ų buried · 46 hydrogen bonds · protein-protein
- D–E · 1993 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 8 modified (disulfide, methylation).
Compared structures
- 7JN4 · Rubisco in the apo state · the same entry in another collection · chain P against P, 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 A0A218N8A3
- Every structure of UniProt P08475
- Elsewhere: RCSB PDB 7JN4 · PDBe 7JN4 · UniProt A0A218N8A3 · UniProt P08475
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