› 5zym

X-ray diffraction
1.9Å resolution

Crystal structure of CERT START domain in complex with compound E25B

Released:
DOI: 10.2210/pdb5zym/pdb
PDB entry 5zym coloured by chain, front view.
PDB entry 5zym coloured by chain, side view.
PDB entry 5zym coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Natural ligand-nonmimetic inhibitors of the lipid-transfer protein CERT
Nakao N, Ueno M, Sakai S, Egawa D, Hanzawa H, Kawasaki S, Kumagai K, Suzuki M, Kobayashi S, Hanada K
Commun Chem (2019)

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-195280 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ceramide transfer protein Chain: A
Molecule details ›
Chain: A
Length: 237 amino acids
Theoretical weight: 27.06 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9Y5P4 (Residues: 390-624; Coverage: 38%)
Gene names: CERT, CERT1, COL4A3BP, STARD11
Sequence domains: START domain
Structure domains: Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4

Ligands and Environments

2 bound ligands:
Ligand 9M6 1 x 9M6
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P41212
Unit cell:
a: 59.868Å b: 59.868Å c: 153.757Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.182 0.18 0.228
Expression system: Escherichia coli BL21(DE3)

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