MolNFT v1 · #181270 · protein

Crystal structure of cryptococcus neoformans sterylglucosidase 1 with hit 9

7LPQ · Cytoplasmic protein: “Crystal structure of cryptococcus neoformans sterylglucosidase 1 with hit 9”. X-ray diffraction, 2 ligands (YAJ, MG), 20 pockets (best druggability 0.85). MolNFT v1 #181270 on GenesisL1: 3D structure, binding…

PDB: 7LPQ
Type: protein
Length: 2,906 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytoplasmic protein
UniProt: J9W473
Ligands: YAJ, MG
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 4 distinct chains · 33% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cytoplasmic protein	protein	725	33% helix, 22% strand	J9W473
B	Cytoplasmic protein	protein	728	32% helix, 21% strand	J9W473
C	Cytoplasmic protein	protein	727	33% helix, 22% strand	J9W473
D	Cytoplasmic protein	protein	726	33% helix, 22% strand	J9W473

Ligands and binding sites

YAJ · ~{N}-[(3~{R},5~{S})-5-(hydroxymethyl)-1-methyl-pyrrolidin-3-yl]-2-(3-oxidanylidene-4~{H}-1,4-benzoxazin-6-yl)ethanamide · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · chains A, B
GOL · Glycerol · additive · 5 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, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	912	0.85	0.87	110	empty
2	1158	0.85	0.86	96	YAJ
3	1078	0.85	0.85	87	YAJ
4	1137	0.84	0.85	90	YAJ
5	1155	0.84	0.85	93	YAJ

Interfaces

5 interfaces between chains.

B–C · 700 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 652 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 520 Å² buried · 1 hydrogen bond · protein-protein
B–D · 85 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 84 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7LPQ · Crystal structure of Cryptococcus neoformans sterylglucosidase 1 with hit 9 · 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 7LPQ · PDBe 7LPQ · UniProt J9W473

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