› 3v1d

X-ray diffraction
1.24Å resolution

Crystal structure of de novo designed MID1-cobalt

Released:
DOI: 10.2210/pdb3v1d/pdb
PDB entry 3v1d coloured by chain, front view.
PDB entry 3v1d coloured by chain, side view.
PDB entry 3v1d coloured by chain, top view.
Source organism: synthetic construct
Primary publication:
Metal-mediated affinity and orientation specificity in a computationally designed protein homodimer.
Der BS, Machius M, Miley MJ, Mills JL, Szyperski T, Kuhlman B
J Am Chem Soc 134 375-85 (2012)
PMID: 22092237

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-164143 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Computational design, MID1-cobalt Chains: A, B, C, D, E, F, G, H
Molecule details ›
Chains: A, B, C, D, E, F, G, H
Length: 48 amino acids
Theoretical weight: 5.5 KDa
Source organism: synthetic construct
Expression system: Escherichia coli BL21
Structure domains: Rabenosyn, Rab binding domain

Ligands and Environments

2 bound ligands:
Ligand CO 8 x CO
Ligand 1PE 4 x 1PE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P1
Unit cell:
a: 27.72Å b: 45.451Å c: 62.112Å
α: 90.04° β: 90° γ: 90°
R-values:
R R work R free
0.147 0.147 0.194
Expression system: Escherichia coli BL21

Quick links

Citations

22 review citations

Protein design: toward functional metalloenzymes.
Yu et al. (2014)
21 more

2 mentions without citation

De novo protein design, a retrospective.
Korendovych et al. (2020)
1 more