› 5e5y

X-ray diffraction
1.51Å resolution

Quasi-racemic snakin-1 in P1 before radiation damage

Released:
DOI: 10.2210/pdb5e5y/pdb
PDB entry 5e5y coloured by chain, front view.
PDB entry 5e5y coloured by chain, side view.
PDB entry 5e5y coloured by chain, top view.
Source organism: Solanum tuberosum
Primary publication:
Radiation Damage and Racemic Protein Crystallography Reveal the Unique Structure of the GASA/Snakin Protein Superfamily.
Yeung H, Squire CJ, Yosaatmadja Y, Panjikar S, López G, Molina A, Baker EN, Harris PW, Brimble MA
Angew Chem Int Ed Engl 55 7930-3 (2016)
PMID: 27145301

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-188202 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Snakin-1 Chains: A, C
Molecule details ›
Chains: A, C
Length: 63 amino acids
Theoretical weight: 7.06 KDa
Source organism: Solanum tuberosum
Expression system: Not provided
UniProt:
  • Canonical: Q948Z4 (Residues: 26-88; Coverage: 100%)
Gene name: SN1
Sequence domains: Gibberellin regulated protein
Snakin-1 Chains: B, D
Molecule details ›
Chains: B, D
Length: 63 amino acids
Theoretical weight: 6.94 KDa
Source organism: Solanum tuberosum
Expression system: Not provided
UniProt:
  • Canonical: Q948Z4 (Residues: 26-88; Coverage: 100%)
Gene name: SN1
Sequence domains: Gibberellin regulated protein

Ligands and Environments

2 bound ligands:
Ligand EDO 5 x EDO
Ligand FMT 6 x FMT
17 modified residues:
Ligand PHI 2 x PHI
Ligand DSN 12 x DSN
Ligand DSG 6 x DSG
Ligand DPN 2 x DPN
Ligand DCY 24 x DCY
Ligand DAS 6 x DAS
Ligand DLY 22 x DLY
Ligand DLE 6 x DLE
Ligand DAR 6 x DAR
Ligand DAL 4 x DAL
Ligand DTY 6 x DTY
Ligand DIL 2 x DIL
Ligand DGL 6 x DGL
Ligand DVA 2 x DVA
Ligand DPR 6 x DPR
Ligand DTH 2 x DTH
Ligand DHI 2 x DHI

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: P1
Unit cell:
a: 31.233Å b: 37.415Å c: 50.303Å
α: 93° β: 90.58° γ: 102.57°
R-values:
R R work R free
0.182 0.179 0.226
Expression system: Not provided

Quick links

Citations

5 review citations

Molecular and Biological Properties of Snakins: The Foremost Cysteine-Rich Plant Host Defense Peptides.
Su et al. (2020)
4 more

1 mention without citation

Plant antimicrobial peptides: structures, functions, and applications.
Li et al. (2021)