MolNFT v1 · #85395 · protein
ATP-triggered molecular mechanics of the chaperonin groel
4AB3 · 60 kda chaperonin: “ATP-triggered molecular mechanics of the chaperonin groel”. Electron microscopy, 3 ligands (ATP, MG, PO4), 20 pockets (best druggability 0.81). MolNFT v1 #85395 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4AB3
- 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 0.81
Structure
electron microscopy · 1 distinct chain · 52% helix, 15% 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 | 52% helix, 15% 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 | 919 | 0.81 | 0.83 | 96 | PO4, MG, ATP |
| 2 | 932 | 0.79 | 0.81 | 106 | PO4, MG, ATP |
| 3 | 924 | 0.79 | 0.81 | 105 | PO4, MG, ATP |
| 4 | 1121 | 0.79 | 0.81 | 107 | PO4, MG, ATP |
| 5 | 1169 | 0.79 | 0.80 | 106 | PO4, MG, ATP |
Interfaces
21 interfaces between chains.
- K–L · 1119 Ų buried · 18 hydrogen bonds · protein-protein
- H–I · 1109 Ų buried · 18 hydrogen bonds · protein-protein
- I–J · 1108 Ų buried · 20 hydrogen bonds · protein-protein
- J–K · 1108 Ų buried · 19 hydrogen bonds · protein-protein
- M–N · 1107 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4AB3 · ATP-triggered molecular mechanics of the chaperonin GroEL · 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 P0A6F5
- Elsewhere: RCSB PDB 4AB3 · PDBe 4AB3 · UniProt P0A6F5
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