Research workbench
Visualizing groel-es in the act of encapsulating a non-native substrate protein
Analyse Visualizing groel-es in the act of encapsulating a non-native substrate protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZQ0
- Type
- protein
- Length
- 8,015 residues
- Chains
- 21
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 60 kda chaperonin; 10 kda chaperonin
- UniProt
- P0A6F5, P0A6F9
- Ligands
- ADP, MG
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 2 distinct chains · 44% helix, 20% 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 | 51% helix, 17% strand | P0A6F5 |
| O, P, Q, R, S, T, U | 10 kda chaperonin | protein | 97 | 3% helix, 37% strand | P0A6F9 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 7 copies · chains A, B, C, D, E, F, G
- MG · Magnesium ion · metal · 7 copies · chains A, B, C, D, E, F, G
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 | 724 | 0.81 | 0.85 | 93 | ADP, MG |
| 2 | 702 | 0.80 | 0.84 | 84 | ADP, MG |
| 3 | 399 | 0.80 | 0.89 | 69 | ADP, MG |
| 4 | 681 | 0.80 | 0.84 | 89 | ADP, MG |
| 5 | 396 | 0.79 | 0.89 | 60 | ADP, MG |
Interfaces
49 interfaces between chains.
- F–G · 1860 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1793 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 1784 Ų buried · 23 hydrogen bonds · protein-protein
- J–K · 1779 Ų buried · 25 hydrogen bonds · protein-protein
- H–N · 1753 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 3ZQ0 · Visualizing GroEL-ES in the Act of Encapsulating a Non-Native Substrate Protein · 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
- Every structure of UniProt P0A6F5
- Every structure of UniProt P0A6F9
- Elsewhere: RCSB PDB 3ZQ0 · PDBe 3ZQ0 · UniProt P0A6F5 · UniProt P0A6F9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.