Research workbench
Subtomogram averaging of rubisco from cyanobium carboxysome
Analyse Subtomogram averaging of rubisco from cyanobium carboxysome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ZC1
- Type
- protein
- Length
- 4,416 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
- A5CKD0, B5ILN2
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J, M, P, S, V | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 445 | 43% helix, 17% strand | A5CKD0 |
| B, E, H, K, N, Q, T, W | Ribulose bisphosphate carboxylase, small subunit | protein | 107 | 28% helix, 24% strand | B5ILN2 |
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 | 123 | 0.81 | 0.98 | 36 | empty |
| 2 | 930 | 0.79 | 0.82 | 96 | empty |
| 3 | 840 | 0.79 | 0.82 | 88 | empty |
| 4 | 805 | 0.79 | 0.82 | 77 | empty |
| 5 | 811 | 0.78 | 0.82 | 81 | empty |
Interfaces
48 interfaces between chains.
- J–S · 3852 Ų buried · 37 hydrogen bonds · protein-protein
- A–P · 3849 Ų buried · 36 hydrogen bonds · protein-protein
- D–M · 3807 Ų buried · 32 hydrogen bonds · protein-protein
- G–V · 3735 Ų buried · 32 hydrogen bonds · protein-protein
- J–K · 1252 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7ZC1 · Subtomogram averaging of Rubisco from Cyanobium carboxysome · the same entry in another collection · 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 A5CKD0
- Every structure of UniProt B5ILN2
- Elsewhere: RCSB PDB 7ZC1 · PDBe 7ZC1 · UniProt A5CKD0 · UniProt B5ILN2
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