› 4k3h

X-ray diffraction
2.45Å resolution

Immunoglobulin lambda variable domain L5(L89S) fluorogen activationg protein in complex with malachite green

Released:
DOI: 10.2210/pdb4k3h/pdb
PDB entry 4k3h coloured by chain, front view.
PDB entry 4k3h coloured by chain, side view.
PDB entry 4k3h coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Malachite green mediates homodimerization of antibody VL domains to form a fluorescent ternary complex with singular symmetric interfaces.
Szent-Gyorgyi C, Stanfield RL, Andreko S, Dempsey A, Ahmed M, Capek S, Waggoner AS, Wilson IA, Bruchez MP
J Mol Biol 425 4595-613 (2013)
PMID: 23978698

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-213523 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Immunoglobulin lambda variable domain L5(L89S) Chains: A, B, C, D, E, F, G, H
Molecule details ›
Chains: A, B, C, D, E, F, G, H
Length: 118 amino acids
Theoretical weight: 12.53 KDa
Source organism: Homo sapiens
Expression system: Saccharomyces cerevisiae
Structure domains: Immunoglobulins

Ligands and Environments

3 bound ligands:
Ligand 1OM 4 x 1OM
Ligand GOL 12 x GOL
Ligand MAN 3 x MAN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL11-1
Spacegroup: P43
Unit cell:
a: 94.11Å b: 94.11Å c: 175.8Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.196 0.194 0.225
Expression system: Saccharomyces cerevisiae

Quick links

Citations

6 review citations

Structural Principles of Fluorescent RNA Aptamers.
Trachman et al. (2017)
5 more

1 mention without citation

Malachite green mediates homodimerization of antibody VL domains to form a fluorescent ternary complex with singular symmetric interfaces.
Szent-Gyorgyi et al. (2013)