MolNFT v1 · #34634 · protein
Thermodynamic penalty arising from burial of a ligand polar group within a hydrophobic pocket of a protein receptor
2DM5 · Major urinary protein: “Thermodynamic penalty arising from burial of a ligand polar group within a hydrophobic pocket of a protein…”. X-ray diffraction, 2 ligands (ODI, CD), 1 pocket (best druggability 0.82). MolNFT v1 #34634 on…
- PDB
- 2DM5
- Type
- protein
- Length
- 157 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major urinary protein
- UniProt
- P11589
- Ligands
- ODI, CD
- Pockets
- 1 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Major urinary protein | protein | 157 | 15% helix, 47% strand | P11589 |
Ligands and binding sites
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 | 124 | 0.82 | 0.98 | 23 | ODI |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2DM5 · Thermodynamic Penalty Arising From Burial of a Ligand Polar Group Within a Hydrophobic… · the same entry in another collection · chain A against A, TM-score 1.00
- P11589 · AlphaFold monomer V2.0 prediction for major urinary protein 2 (P11589) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P11589
- Elsewhere: RCSB PDB 2DM5 · PDBe 2DM5 · UniProt P11589
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