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Crystal structure of the sterol-bound second start domain of yeast LAM4

Analyse Crystal structure of the sterol-bound second start domain of yeast LAM4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6BYM
Type: protein
Length: 395 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sterol-binding protein
UniProt: A0A250WL92
Ligands: HC3
Pockets: 3 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 26% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sterol-binding protein	protein	200	24% helix, 33% strand	A0A250WL92
B	Sterol-binding protein	protein	195	27% helix, 33% strand	A0A250WL92

Ligands and binding sites

HC3 · 25-hydroxycholesterol · ligand · 2 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	404	0.83	0.91	48	HC3
2	1059	0.81	0.82	100	HC3
3	175	0.47	0.76	24	empty

Interfaces

1 interface between chains.

A–B · 959 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

6BYM · Crystal structure of the sterol-bound second StART domain of yeast Lam4 · 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 A0A250WL92
Elsewhere: RCSB PDB 6BYM · PDBe 6BYM · UniProt A0A250WL92

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