› 6b9j

X-ray diffraction
2.9Å resolution

Structure of vaccinia virus D8 protein bound to human Fab vv138

Released:
DOI: 10.2210/pdb6b9j/pdb
PDB entry 6b9j coloured by chain, front view.
PDB entry 6b9j coloured by chain, side view.
PDB entry 6b9j coloured by chain, top view.
Source organisms:
Primary publication:
Structure-function characterization of three human antibodies targeting the vaccinia virus adhesion molecule D8.
Matho MH, Schlossman A, Gilchuk IM, Miller G, Mikulski Z, Hupfer M, Wang J, Bitra A, Meng X, Xiang Y, Kaever T, Doukov T, Ley K, Crotty S, Peters B, Hsieh-Wilson LC, Crowe JE, Zajonc DM
J Biol Chem 293 390-401 (2018)
PMID: 29123031

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-231365 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Cell surface-binding protein OPG105 Chains: X, Y
Molecule details ›
Chains: X, Y
Length: 241 amino acids
Theoretical weight: 27.97 KDa
Source organism: Vaccinia virus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q1M1K6 (Residues: 1-235; Coverage: 77%)
Gene names: VACAC2_124, VACCL3_124, VAC_DPP17_124, VACli_124, synVACV_124
Sequence domains: Eukaryotic-type carbonic anhydrase
Structure domains: Alpha carbonic anhydrase
Fab vv138 Heavy chain Chains: A, H
Molecule details ›
Chains: A, H
Length: 217 amino acids
Theoretical weight: 23.21 KDa
Source organism: Homo sapiens
Structure domains: Immunoglobulins
Fab vv138 Light chain Chains: B, L
Molecule details ›
Chains: B, L
Length: 215 amino acids
Theoretical weight: 23.44 KDa
Source organism: Homo sapiens
Structure domains: Immunoglobulins

Ligands and Environments

2 bound ligands:
Ligand GOL 2 x GOL
Ligand NA 7 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL7-1
Spacegroup: C2221
Unit cell:
a: 234.282Å b: 253.842Å c: 73.76Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.243 0.241 0.269
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

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Xiang et al. (2022)
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4 mentions without citation

Neutralization Determinants on Poxviruses.
Riccardo et al. (2023)
3 more