Research workbench
Rubisco from thalassiosira antarctica
Analyse Rubisco from thalassiosira antarctica in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MZ2
- Type
- protein
- Length
- 4,959 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rubisco large subunit; Rubisco small subunit
- Ligands
- CAP, MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H, F, E | Rubisco large subunit | protein | 481 | 42% helix, 16% strand | — |
| C, B | Rubisco large subunit | protein | 480 | 42% helix, 16% strand | — |
| D | Rubisco large subunit | protein | 482 | 42% helix, 16% strand | — |
| G | Rubisco large subunit | protein | 481 | 42% helix, 16% strand | — |
| I, O, L, N, M, P, J, K | Rubisco small subunit | protein | 139 | 23% helix, 29% strand | — |
Ligands and binding sites
- CAP · 2-carboxyarabinitol-1,5-diphosphate · ligand · 8 copies · chains A, B, C, D, H, G, F, E
- MG · Magnesium ion · metal · 10 copies · chains A, B, C, D, H, G, F, E, I, J, K, O, N, P
- EDO · 1,2-ethanediol · additive · 22 copies · chains A, G, I, H, F, N, D, B, P, J, L, C, O, E, K, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 378 | 0.87 | 0.96 | 66 | empty |
| 2 | 375 | 0.87 | 0.96 | 66 | empty |
| 3 | 277 | 0.85 | 0.96 | 46 | empty |
| 4 | 270 | 0.84 | 0.96 | 50 | EDO |
| 5 | 268 | 0.84 | 0.96 | 53 | empty |
Interfaces
56 interfaces between chains.
- A–B · 4909 Ų buried · 92 hydrogen bonds · protein-protein
- C–D · 4906 Ų buried · 96 hydrogen bonds · protein-protein
- H–G · 4905 Ų buried · 93 hydrogen bonds · protein-protein
- F–E · 4897 Ų buried · 94 hydrogen bonds · protein-protein
- F–N · 1592 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 64 modified (nonstandard, hydroxylation, carboxylation, methylation, oxidation).
Compared structures
- 5MZ2 · Rubisco from Thalassiosira antarctica · 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
- Elsewhere: RCSB PDB 5MZ2 · PDBe 5MZ2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.