MolNFT v1 · #181269 · protein

Crystal structure of cryptococcus neoformans sterylglucosidase 1 with hit 1

7LPP · Cytoplasmic protein: “Crystal structure of cryptococcus neoformans sterylglucosidase 1 with hit 1”. X-ray diffraction, 2 ligands (YAG, MG), 20 pockets (best druggability 0.86). MolNFT v1 #181269 on GenesisL1: 3D structure, binding…

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.

Pocket	Volume (Å³)	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 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 692 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 560 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 100 Å² buried · 1 hydrogen bond · protein-protein
A–C · 97 Å² 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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