Research workbench
Crystal structure of the possum milk whey lipocalin trichosurin at pH 4.6 with bound 4-ethylphenol
Analyse Crystal structure of the possum milk whey lipocalin trichosurin at pH 4.6 with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2RA6
- Type
- protein
- Length
- 569 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trichosurin
- UniProt
- Q29147
- Ligands
- ETY, ZN, CL
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trichosurin | protein | 141 | 15% helix, 51% strand | Q29147 |
| B | Trichosurin | protein | 142 | 15% helix, 51% strand | Q29147 |
| C, D | Trichosurin | protein | 143 | 15% helix, 51% strand | Q29147 |
Ligands and binding sites
- ETY · 4-ethylphenol · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D
- CL · Chloride ion · ion · 9 copies · chains A, B, C, D
- IPA · Isopropyl alcohol · additive · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1149 | 0.82 | 0.83 | 97 | CL |
| 2 | 83 | 0.78 | 0.99 | 20 | ETY, IPA |
| 3 | 86 | 0.78 | 0.98 | 18 | ETY, IPA |
| 4 | 56 | 0.73 | 0.98 | 15 | ETY |
| 5 | 61 | 0.73 | 0.97 | 15 | ETY |
Interfaces
5 interfaces between chains.
- C–D · 1002 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 977 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 327 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 320 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 83 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2RA6 · Crystal Structure of the Possum Milk Whey Lipocalin Trichosurin at pH 4.6 with Bound… · the same entry in another collection · chain A against A, TM-score 1.00
- Q29147 · AlphaFold monomer V2.0 prediction for trichosurin (Q29147) · a predicted model of the same protein · chain C 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 Q29147
- Elsewhere: RCSB PDB 2RA6 · PDBe 2RA6 · UniProt Q29147
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