Research workbench
Groel at sub-nanometer resolution by constrained single particle tomography
Analyse Groel at sub-nanometer resolution by constrained single particle tomography in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YNJ
- Type
- protein
- Length
- 7,336 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 60 kda chaperonin
- UniProt
- Q1R3B6
- Ligands
- AGS, TL, MG
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 1 distinct chain · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N | 60 kda chaperonin | protein | 524 | 50% helix, 18% strand | Q1R3B6 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 14 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N
- TL · Thallium (I) ion · metal · 56 copies · chains A, H, B, C, D, E, F, G, N, I, J, K, L, M
- MG · Magnesium ion · metal · 14 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N
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 | 1024 | 0.79 | 0.81 | 92 | AGS, TL, MG |
| 2 | 1053 | 0.79 | 0.80 | 97 | AGS, TL, MG |
| 3 | 989 | 0.79 | 0.80 | 94 | AGS, MG |
| 4 | 744 | 0.79 | 0.83 | 78 | AGS, TL, MG |
| 5 | 1044 | 0.78 | 0.80 | 99 | AGS, TL, MG |
Interfaces
28 interfaces between chains.
- M–N · 1608 Ų buried · 7 hydrogen bonds · protein-protein
- L–M · 1607 Ų buried · 7 hydrogen bonds · protein-protein
- G–I · 1606 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 1606 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 1606 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2YNJ · GroEL at sub-nanometer resolution by Constrained Single Particle Tomography · the same entry in another collection · chain K against K, 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 Q1R3B6
- Elsewhere: RCSB PDB 2YNJ · PDBe 2YNJ · UniProt Q1R3B6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.