Research workbench

Crystal structure of the first start-like domain of YSP2P/LAM2P in its apo and ergosterol-bound state.

Analyse Crystal structure of the first start-like domain of YSP2P/LAM2P in its apo and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6CAY
Type: protein
Length: 661 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sterol-binding protein
UniProt: A0A250W8A7
Ligands: ERG
Pockets: 13 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 31% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sterol-binding protein	protein	165	31% helix, 39% strand	A0A250W8A7
B, C	Sterol-binding protein	protein	165	32% helix, 39% strand	A0A250W8A7
D	Sterol-binding protein	protein	166	30% helix, 39% strand	A0A250W8A7

Ligands and binding sites

ERG · Ergosterol · ligand · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	426	0.79	0.87	47	ERG
2	454	0.78	0.86	46	ERG
3	842	0.74	0.78	61	empty
4	374	0.72	0.83	48	empty
5	308	0.70	0.83	39	empty

Interfaces

5 interfaces between chains.

A–C · 870 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 844 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 632 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 607 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 36 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified (engineered).

Compared structures

6CAY · Crystal structure of the first StART-like domain of Ysp2p/Lam2p in its apo and… · 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 A0A250W8A7
Elsewhere: RCSB PDB 6CAY · PDBe 6CAY · UniProt A0A250W8A7

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.