› 6al0

X-ray diffraction
2.6Å resolution

The NZ-1 Fab complexed with the PDZ tandem fragment of A. aeolicus S2P homolog with the PA12 tag inserted between the residues 263 and 267

Released:
DOI: 10.2210/pdb6al0/pdb
Model geometry
Fit model/data
PDB entry 6al0 coloured by chain, front view.
PDB entry 6al0 coloured by chain, side view.
PDB entry 6al0 coloured by chain, top view.
Source organisms:
Primary publication:
Application of the NZ-1 Fab as a crystallization chaperone for PA tag-inserted target proteins.
Tamura R, Oi R, Akashi S, Kaneko MK, Kato Y, Nogi T
Protein Sci 28 823-836 (2019)
PMID: 30666745

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-208136 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Putative zinc metalloprotease aq_1964 Chain: A
Molecule details ›
Chain: A
Length: 189 amino acids
Theoretical weight: 20.82 KDa
Source organism: Aquifex aeolicus VF5
Expression system: Escherichia coli
UniProt:
  • Canonical: O67776 (Residues: 115-264, 265-266, 267-292; Coverage: 42%)
Gene name: aq_1964
Sequence domains:
Structure domains: Pdz3 Domain
Light chain of antigen binding fragment, Fab of NZ-1 Chain: L
Molecule details ›
Chain: L
Length: 214 amino acids
Theoretical weight: 23.35 KDa
Source organism: Rattus norvegicus
Expression system: Mus musculus
Structure domains: Immunoglobulins
Heavy chain of antigen binding fragment, Fab of NZ-1 Chain: H

Ligands and Environments

No bound ligands
2 modified residues:
Ligand SNN 1 x SNN
Ligand PCA 1 x PCA

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: PHOTON FACTORY BEAMLINE BL-1A
Spacegroup: P4212
Unit cell:
a: 141.663Å b: 141.663Å c: 78.62Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.201 0.199 0.251
Expression systems:
  • Escherichia coli
  • Mus musculus

Quick links

Citations

1 review citation

Roles of Podoplanin in Malignant Progression of Tumor.
Suzuki et al. (2022)
12 other articles

3 mentions without citation

An expanded benchmark for antibody-antigen docking and affinity prediction reveals insights into antibody recognition determinants.
Guest et al. (2021)
2 more