Research workbench
Crystal structure of cryptococcus neoformans sterylglucosidase 1 with hit 1
Analyse Crystal structure of cryptococcus neoformans sterylglucosidase 1 with hit 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LPP
- Type
- protein
- Length
- 2,907 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytoplasmic protein
- UniProt
- J9W473
- Ligands
- YAG, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytoplasmic protein | protein | 732 | 32% helix, 21% strand | J9W473 |
| B | Cytoplasmic protein | protein | 727 | 32% helix, 20% strand | J9W473 |
| C | Cytoplasmic protein | protein | 729 | 32% helix, 21% strand | J9W473 |
| D | Cytoplasmic protein | protein | 719 | 33% helix, 20% strand | J9W473 |
Ligands and binding sites
- YAG · 4-(hydroxymethyl)-1-[[2-(3-methoxyphenyl)-1,3-thiazol-5-yl]methyl]piperidin-4-ol · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · chains B, C
- GOL · Glycerol · additive · 4 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1017 | 0.86 | 0.87 | 92 | YAG |
| 2 | 973 | 0.86 | 0.87 | 112 | empty |
| 3 | 1092 | 0.85 | 0.85 | 93 | YAG |
| 4 | 1171 | 0.84 | 0.85 | 90 | YAG |
| 5 | 1139 | 0.84 | 0.85 | 88 | YAG |
Interfaces
5 interfaces between chains.
- C–D · 806 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 692 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 560 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 100 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 97 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7LPP · Crystal structure of Cryptococcus neoformans sterylglucosidase 1 with hit 1 · 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 J9W473
- Elsewhere: RCSB PDB 7LPP · PDBe 7LPP · UniProt J9W473
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