Research workbench
Heat shock protein 70 substrate binding domain with covalently linked novolactone
Analyse Heat shock protein 70 substrate binding domain with covalently linked… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WV7
- Type
- protein
- Length
- 280 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heat shock 70 kda protein 1A/1B
- UniProt
- P08107
- Ligands
- 3UM
- Pockets
- 5 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heat shock 70 kda protein 1A/1B | protein | 145 | 19% helix, 44% strand | P08107 |
| B | Heat shock 70 kda protein 1A/1B | protein | 135 | 12% helix, 47% strand | P08107 |
Ligands and binding sites
- 3UM · (5beta,6alpha,8alpha,14alpha)-13-ethenyl-5,6-dihydroxy-14-methylpodocarp-12-en-15-oic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 167 | 0.52 | 0.78 | 19 | 3UM |
| 2 | 226 | 0.50 | 0.76 | 26 | empty |
| 3 | 165 | 0.50 | 0.77 | 19 | 3UM |
| 4 | 92 | 0.38 | 0.77 | 22 | empty |
| 5 | 96 | 0.36 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 636 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4WV7 · Heat shock protein 70 substrate binding domain with covalently linked novolactone · the same entry in another collection · chain A against A, 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 P08107
- Elsewhere: RCSB PDB 4WV7 · PDBe 4WV7 · UniProt P08107
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