Research workbench
Closed state cryoem reconstruction of HSP104:ATPYS and fitc casein
Analyse Closed state cryoem reconstruction of HSP104:ATPYS and fitc casein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VJH
- Type
- protein
- Length
- 3,485 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heat shock protein 104; Fitc casein
- UniProt
- P31539
- Ligands
- AGS
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Heat shock protein 104 | protein | 579 | 50% helix, 12% strand | P31539 |
| F | Heat shock protein 104 | protein | 564 | 51% helix, 13% strand | P31539 |
| P | Fitc casein | protein | 26 | 0% helix, 15% strand | — |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 12 copies · chains A, F, B, C, D, E
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 | 881 | 0.86 | 0.88 | 88 | empty |
| 2 | 634 | 0.86 | 0.91 | 82 | empty |
| 3 | 456 | 0.85 | 0.93 | 74 | AGS |
| 4 | 854 | 0.84 | 0.87 | 84 | empty |
| 5 | 400 | 0.83 | 0.91 | 63 | AGS |
Interfaces
17 interfaces between chains.
- D–E · 4469 Ų buried · 64 hydrogen bonds · protein-protein
- C–D · 4401 Ų buried · 63 hydrogen bonds · protein-protein
- B–C · 4204 Ų buried · 62 hydrogen bonds · protein-protein
- A–B · 3083 Ų buried · 42 hydrogen bonds · protein-protein
- E–F · 2441 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 5VJH · Closed State CryoEM Reconstruction of Hsp104:ATPyS and FITC casein · the same entry in another collection · chain P against P, TM-score 1.00
- P31539 · AlphaFold monomer V2.0 prediction for heat shock protein 104 (P31539) · a predicted model of the same protein · chain A against A, TM-score 0.84
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 P31539
- Elsewhere: RCSB PDB 5VJH · PDBe 5VJH · UniProt P31539
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