› 3dz4

X-ray diffraction
1.84Å resolution

Human AdoMetDC with 5'-[(2-carboxamidoethyl)methylamino]-5'-deoxy-8-methyladenosine

Released:
DOI: 10.2210/pdb3dz4/pdb
PDB entry 3dz4 coloured by chain, front view.
PDB entry 3dz4 coloured by chain, side view.
PDB entry 3dz4 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
New insights into the design of inhibitors of human S-adenosylmethionine decarboxylase: studies of adenine C8 substitution in structural analogues of S-adenosylmethionine.
McCloskey DE, Bale S, Secrist JA, Tiwari A, Moss TH, Valiyaveettil J, Brooks WH, Guida WC, Pegg AE, Ealick SE
OpenAccess logo J Med Chem 52 1388-407 (2009)
PMID: 19209891

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine = S-adenosyl 3-(methylthio)propylamine + CO(2)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-148140 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
S-adenosylmethionine decarboxylase beta chain Chain: B
Molecule details ›
Chain: B
Length: 67 amino acids
Theoretical weight: 7.69 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P17707 (Residues: 1-67; Coverage: 20%)
Gene names: AMD, AMD1
Structure domains: S-adenosylmethionine decarboxylase
S-adenosylmethionine decarboxylase alpha chain Chain: A
Molecule details ›
Chain: A
Length: 267 amino acids
Theoretical weight: 30.69 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P17707 (Residues: 69-334; Coverage: 80%)
Gene names: AMD, AMD1
Sequence domains: Adenosylmethionine decarboxylase
Structure domains: S-adenosylmethionine decarboxylase

Ligands and Environments

2 bound ligands:
Ligand PUT 1 x PUT
Ligand C8M 1 x C8M
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE A1
Spacegroup: C2
Unit cell:
a: 99.818Å b: 50.949Å c: 68.985Å
α: 90° β: 105.52° γ: 90°
R-values:
R R work R free
0.204 0.204 0.237
Expression system: Escherichia coli

Quick links

Citations

4 review citations

S-Adenosylmethionine decarboxylase.
Pegg AE. (2009)
3 more

2 mentions without citation

New insights into the design of inhibitors of human S-adenosylmethionine decarboxylase: studies of adenine C8 substitution in structural analogues of S-adenosylmethionine.
McCloskey et al. (2009)
1 more