› 5k8g

X-ray diffraction
2Å resolution

Crystal structure of a putative peptide-binding domain of MpAFP

Released:
DOI: 10.2210/pdb5k8g/pdb
PDB entry 5k8g coloured by chain, front view.
PDB entry 5k8g coloured by chain, side view.
PDB entry 5k8g coloured by chain, top view.
Source organism: Marinomonas primoryensis
Primary publication:
Structure of a 1.5-MDa adhesin that binds its Antarctic bacterium to diatoms and ice.
Guo S, Stevens CA, Vance TDR, Olijve LLC, Graham LA, Campbell RL, Yazdi SR, Escobedo C, Bar-Dolev M, Yashunsky V, Braslavsky I, Langelaan DN, Smith SP, Allingham JS, Voets IK, Davies PL
Sci Adv 3 e1701440 (2017)
PMID: 28808685

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-106747 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Cadherin-like domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 540 amino acids
Theoretical weight: 56.61 KDa
Source organism: Marinomonas primoryensis
Expression system: Escherichia coli
UniProt:
  • Canonical: A1YIY3 (Residues: 205-723; Coverage: 33%)

Ligands and Environments

1 bound ligand:
Ligand CA 16 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08ID-1
Spacegroup: P1
Unit cell:
a: 50.115Å b: 61.065Å c: 63.473Å
α: 66.25° β: 72.66° γ: 67.94°
R-values:
R R work R free
0.185 0.183 0.221
Expression system: Escherichia coli

Quick links

Citations

12 review citations

Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases.
Tørresen et al. (2019)
11 more

4 mentions without citation

Structural insight reveals SARS-CoV-2 ORF7a as an immunomodulating factor for human CD14+ monocytes.
Zhou et al. (2021)
3 more