Research workbench
Van der waals interactions dominate hydrophobic association in a protein binding site occluded from solvent water
Analyse Van der waals interactions dominate hydrophobic association in a protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YP6
- Type
- protein
- Length
- 157 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major urinary protein 1
- UniProt
- P11588
- Ligands
- PRZ, CD, CL
- Pockets
- 1 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Major urinary protein 1 | protein | 157 | 15% helix, 47% strand | P11588 |
Ligands and binding sites
- PRZ · 2-isobutyl-3-methoxypyrazine · ligand · chains A
- CD · Cadmium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.81 | 0.98 | 24 | PRZ |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1YP6 · Van der Waals Interactions Dominate Hydrophobic Association in a Protein Binding Site… · the same entry in another collection · chain A against A, TM-score 1.00
- P11588 · AlphaFold monomer V2.0 prediction for major urinary protein 1 (P11588) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P11588
- Elsewhere: RCSB PDB 1YP6 · PDBe 1YP6 · UniProt P11588
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