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Crystal structure of cert start domain in complex with compound E25

Analyse Crystal structure of cert start domain in complex with compound E25 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5ZYK
Type: protein
Length: 231 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lipid-transfer protein cert
UniProt: Q9Y5P4
Ligands: 9MC
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	231	26% helix, 39% strand	Q9Y5P4

Ligands and binding sites

9MC · 2-[4-[4-cyclopentyl-3-[(1~{S},2~{R})-2-pyridin-2-ylcyclopropyl]phenyl]phenyl]sulfonylethanol · 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	514	0.85	0.91	44	9MC
2	61	0.30	0.75	16	empty
3	62	0.29	0.74	18	empty

Compared structures

5ZYK · Crystal structure of CERT START domain in complex with compound E25 · 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 5ZYK · PDBe 5ZYK · UniProt Q9Y5P4

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