MolNFT v2 · #221781 · protein
Firmicutes Rubisco
8U66: “Firmicutes Rubisco”. Electron microscopy at 2.21, 2 ligands (CAP, MG), 20 pockets (best druggability 0.81). MolNFT v2 #221781 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 8U66
- Type
- protein
- Length
- 3,584 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.21
- Source
- Bacillota
- Molecule
- Rubisco
- Ligands
- CAP, MG
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · resolution 2.21 · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Rubisco | protein | 448 | 45% helix, 17% strand | — |
Ligands and binding sites
- CAP · 2-carboxyarabinitol-1,5-diphosphate · sugar · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
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 | 154 | 0.81 | 0.98 | 46 | MG, CAP |
| 2 | 150 | 0.81 | 0.98 | 46 | CAP |
| 3 | 154 | 0.80 | 0.97 | 45 | CAP |
| 4 | 1143 | 0.80 | 0.82 | 75 | empty |
| 5 | 1130 | 0.80 | 0.82 | 72 | empty |
Interfaces
16 interfaces between chains.
- A–B · 4450 Ų buried · 91 hydrogen bonds · protein-protein
- C–D · 4443 Ų buried · 92 hydrogen bonds · protein-protein
- E–F · 4425 Ų buried · 91 hydrogen bonds · protein-protein
- G–H · 4425 Ų buried · 90 hydrogen bonds · protein-protein
- A–C · 550 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (carboxylation).
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 8U66 · PDBe 8U66
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