Research workbench
Structural analysis of a homolog of programmed cell death 6 protein from leishmania major friedlin
Analyse Structural analysis of a homolog of programmed cell death 6 protein from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y1X
- Type
- protein
- Length
- 356 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leishmania major homolog of programmed cell death 6 protein
- UniProt
- Q9N9M3
- Ligands
- CA, SO4
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leishmania major homolog of programmed cell death 6 protein | protein | 182 | 55% helix, 6% strand | Q9N9M3 |
| B | Leishmania major homolog of programmed cell death 6 protein | protein | 174 | 57% helix, 6% strand | Q9N9M3 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 786 | 0.70 | 0.76 | 51 | empty |
| 2 | 85 | 0.43 | 0.79 | 17 | empty |
| 3 | 78 | 0.41 | 0.79 | 23 | empty |
| 4 | 72 | 0.37 | 0.78 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1573 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 1Y1X · Structural analysis of a homolog of programmed cell death 6 protein from Leishmania major… · 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 Q9N9M3
- Elsewhere: RCSB PDB 1Y1X · PDBe 1Y1X · UniProt Q9N9M3
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