Research workbench
Crystal structure of the WT human mitochondrial chaperonin (ADP:BeF3)14 complex
Analyse Crystal structure of the WT human mitochondrial chaperonin (ADP:BeF3)14 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HT7
- Type
- protein
- Length
- 8,792 residues
- Chains
- 28
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.7
- Source
- Homo sapiens
- Molecule
- 60 kDa heat shock protein, mitochondrial; 10 kDa heat shock protein, mitochondrial
- EC
- 3.6.4.9
- UniProt
- P10809, P61604
- Ligands
- ADP, BEF, MG, K
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · resolution 3.7 · 2 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| J, I, H, N, M, L, K, G, F, E, D, C, B, A | 60 kDa heat shock protein, mitochondrial (EC 3.6.4.9) | protein | 528 | 49% helix, 16% strand | P10809 |
| X, W, V, 2, 1, Z, Y, U, T, S, R, Q, P, O | 10 kDa heat shock protein, mitochondrial | protein | 100 | 3% helix, 41% strand | P61604 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 14 copies · chains J, I, H, N, M, L, K, G, F, E, D, C, B, A
- BEF · Beryllium trifluoride ion · ligand · 14 copies · chains J, I, H, N, M, L, K, G, F, E, D, C, B, A
- MG · Magnesium ion · metal · 14 copies · chains J, I, H, N, M, L, K, G, F, E, D, C, B, A
- K · Potassium ion · metal · 14 copies · chains J, I, H, N, M, L, K, G, F, E, D, C, B, A
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 | 819 | 0.83 | 0.85 | 76 | ADP, BEF, MG, K |
| 2 | 518 | 0.82 | 0.89 | 63 | ADP, BEF, MG, K |
| 3 | 483 | 0.81 | 0.88 | 62 | ADP, BEF, MG, K |
| 4 | 462 | 0.81 | 0.88 | 55 | ADP, BEF, MG, K |
| 5 | 513 | 0.81 | 0.87 | 63 | ADP, BEF, MG, K |
Interfaces
69 interfaces between chains.
- I–H · 1986 Ų buried · 24 hydrogen bonds · protein-protein
- C–B · 1938 Ų buried · 21 hydrogen bonds · protein-protein
- L–K · 1934 Ų buried · 21 hydrogen bonds · protein-protein
- M–L · 1922 Ų buried · 22 hydrogen bonds · protein-protein
- N–M · 1917 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- P10809 · AlphaFold monomer V2.0 prediction for 60 kda heat shock protein, mitochondrial (P10809) · a predicted model of the same protein · chain I against A, TM-score 0.98
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 P10809
- Every structure of UniProt P61604
- Elsewhere: RCSB PDB 6HT7 · PDBe 6HT7 · UniProt P10809 · UniProt P61604
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