Research workbench
ATP-triggered molecular mechanics of the chaperonin groel
Analyse ATP-triggered molecular mechanics of the chaperonin groel in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AB2
- Type
- protein
- Length
- 7,322 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 60 kda chaperonin
- UniProt
- P0A6F5
- Ligands
- ATP, MG, PO4
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 1 distinct chain · 53% helix, 14% 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 | 523 | 53% helix, 14% 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
- PO4 · Phosphate ion · ion · 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 | 829 | 0.82 | 0.84 | 118 | ATP, MG, PO4 |
| 2 | 623 | 0.81 | 0.86 | 90 | ATP, MG, PO4 |
| 3 | 1132 | 0.80 | 0.82 | 132 | ATP, MG, PO4 |
| 4 | 518 | 0.80 | 0.87 | 69 | ATP, MG, PO4 |
| 5 | 1119 | 0.80 | 0.82 | 131 | ATP, MG, PO4 |
Interfaces
21 interfaces between chains.
- D–E · 1278 Ų buried · 31 hydrogen bonds · protein-protein
- A–G · 1278 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1276 Ų buried · 31 hydrogen bonds · protein-protein
- E–F · 1276 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1271 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 4AB2 · ATP-triggered molecular mechanics of the chaperonin GroEL · the same entry in another collection · chain E against E, 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
- Elsewhere: RCSB PDB 4AB2 · PDBe 4AB2 · UniProt P0A6F5
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