› 8pih

X-ray diffraction
1.76Å resolution

Structure of Api m1 in complex with two nanobodies

Released:
DOI: 10.2210/pdb8pih/pdb
PDB entry 8pih coloured by chain, front view.
PDB entry 8pih coloured by chain, side view.
PDB entry 8pih coloured by chain, top view.
Source organisms:
Entry authors: Aagaard JB, Gandini R, Spillner E, Miehe M, Andersen GR

Function and Biology Details

Reaction catalysed: 
Phosphatidylcholine + H(2)O = 1-acylglycerophosphocholine + a carboxylate
Biochemical function:
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-244066 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Phospholipase A2 Chain: A
Molecule details ›
Chain: A
Length: 133 amino acids
Theoretical weight: 15.16 KDa
Source organism: Apis mellifera
UniProt:
  • Canonical: P00630 (Residues: 35-167; Coverage: 89%)
Sequence domains: Phospholipase A2
nanobody AM1-4 Chain: B
Molecule details ›
Chain: B
Length: 127 amino acids
Theoretical weight: 13.61 KDa
Source organism: Lama glama
Expression system: Escherichia coli
nanobdoy AM1-1 Chain: C
Molecule details ›
Chain: C
Length: 118 amino acids
Theoretical weight: 12.89 KDa
Source organism: Lama glama
Expression system: Escherichia coli

Ligands and Environments

1 bound ligand:
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)
Spacegroup: C2
Unit cell:
a: 133.96Å b: 51.33Å c: 73.25Å
α: 90° β: 120.78° γ: 90°
R-values:
R R work R free
0.172 0.171 0.202
Expression system: Escherichia coli

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