Research workbench
Rubisco from skeletonema marinoi
Analyse Rubisco from skeletonema marinoi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FTL
- Type
- protein
- Length
- 2,484 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribulose bisphosphate carboxylase large chain; Ribulose-1,5-bisphosphate…
- EC
- 4.1.1.39
- Ligands
- CAP, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 482 | 41% helix, 16% strand | — |
| I, J, K, L | Ribulose-1,5-bisphosphate CARBOXYLASE/OXYGENASE small subunit | protein | 139 | 23% helix, 32% strand | — |
Ligands and binding sites
- CAP · 2-carboxyarabinitol-1,5-diphosphate · ligand · 4 copies · chains A, C, E, G
- MG · Magnesium ion · metal · 4 copies · chains A, C, E, G
- EDO · 1,2-ethanediol · additive · 18 copies · chains A, I, J, G, C, K, E, L
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 | 814 | 0.81 | 0.84 | 116 | EDO |
| 2 | 231 | 0.79 | 0.93 | 46 | empty |
| 3 | 96 | 0.74 | 0.96 | 23 | empty |
| 4 | 88 | 0.73 | 0.96 | 17 | empty |
| 5 | 104 | 0.73 | 0.94 | 25 | empty |
Interfaces
20 interfaces between chains.
- C–J · 1638 Ų buried · 21 hydrogen bonds · protein-protein
- A–I · 1637 Ų buried · 24 hydrogen bonds · protein-protein
- G–L · 1611 Ų buried · 24 hydrogen bonds · protein-protein
- E–K · 1599 Ų buried · 20 hydrogen bonds · protein-protein
- K–G · 624 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (nonstandard, carboxylation, hydroxylation, methylation).
Compared structures
- 6FTL · Rubisco from Skeletonema marinoi · the same entry in another collection · chain I against I, 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 6FTL · PDBe 6FTL
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