Research workbench
Crystal structure of ygin in complex with menadione
Analyse Crystal structure of ygin in complex with menadione in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TUV
- Type
- protein
- Length
- 103 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein ygin
- UniProt
- P40718
- Ligands
- VK3
- Pockets
- 1 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein ygin | protein | 103 | 35% helix, 32% strand | P40718 |
Ligands and binding sites
- VK3 · Menadione · ligand · 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 | 117 | 0.53 | 0.81 | 15 | VK3 |
Compared structures
- 1TUV · Crystal structure of YgiN in complex with menadione · 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 P40718
- Elsewhere: RCSB PDB 1TUV · PDBe 1TUV · UniProt P40718
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