Research workbench
Structure of the GroEL-ATP complex plunge-frozen 13 ms after mixing with ATP
Analyse Structure of the GroEL-ATP complex plunge-frozen 13 ms after mixing with ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8BLY
- Type
- protein
- Length
- 7,322 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.2
- Source
- Escherichia coli
- Molecule
- Chaperonin GroEL
- EC
- 5.6.1.7
- UniProt
- P0A6F5
- Ligands
- ATP, MG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · resolution 3.2 · 1 distinct chain · 52% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N | Chaperonin GroEL (EC 5.6.1.7) | protein | 523 | 52% helix, 17% strand | P0A6F5 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 14 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N
- 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 | 1065 | 0.82 | 0.83 | 99 | MG, ATP |
| 2 | 1092 | 0.82 | 0.83 | 109 | MG, ATP |
| 3 | 328 | 0.82 | 0.92 | 51 | MG, ATP |
| 4 | 365 | 0.80 | 0.90 | 61 | MG, ATP |
| 5 | 365 | 0.80 | 0.90 | 61 | MG, ATP |
Interfaces
28 interfaces between chains.
- D–F · 2278 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 2271 Ų buried · 29 hydrogen bonds · protein-protein
- C–E · 2270 Ų buried · 29 hydrogen bonds · protein-protein
- H–J · 2259 Ų buried · 26 hydrogen bonds · protein-protein
- B–G · 2257 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 covalent (covalent ligand).
Compared structures
- P0A6F5 · AlphaFold monomer V2.0 prediction for 60 kda chaperonin (P0A6F5) · a predicted model of the same protein · chain J against A, TM-score 0.97
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
- Elsewhere: RCSB PDB 8BLY · PDBe 8BLY · UniProt P0A6F5
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