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Crystal structure of cert start domain in complex with compound D16

Analyse Crystal structure of cert start domain in complex with compound D16 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6IF0
Type: protein
Length: 229 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lipid-transfer protein cert
UniProt: Q9Y5P4
Ligands: A59
Pockets: 3 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 26% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lipid-transfer protein cert	protein	229	26% helix, 39% strand	Q9Y5P4

Ligands and binding sites

A59 · 2-({4'-pentyl-3'-[(Z)-2-(pyridin-2-yl)ethenyl][1,1'-biphenyl]-4-yl}sulfonyl)ethan-1-ol · ligand · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	455	0.85	0.92	44	A59
2	102	0.36	0.74	22	empty
3	52	0.28	0.75	17	empty

Compared structures

6IF0 · Crystal structure of CERT START domain in complex with compound D16 · the same entry in another collection · chain A against A, TM-score 1.00
Q9Y5P4 · AlphaFold monomer V2.0 prediction for ceramide transfer protein (Q9Y5P4) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q9Y5P4
Elsewhere: RCSB PDB 6IF0 · PDBe 6IF0 · UniProt Q9Y5P4

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