› 5ykp

X-ray diffraction
1.68Å resolution

Human methionine aminopeptidase type 1b (F309M mutant) in complex with ovalicin

Released:
DOI: 10.2210/pdb5ykp/pdb
PDB entry 5ykp coloured by chain, front view.
PDB entry 5ykp coloured by chain, side view.
PDB entry 5ykp coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery of natural product ovalicin sensitive type 1 methionine aminopeptidases: molecular and structural basis.
Pillalamarri V, Arya T, Haque N, Bala SC, Marapaka AK, Addlagatta A
Biochem J 476 991-1003 (2019)
PMID: 30837307

Function and Biology Details

Reaction catalysed: 
Release of N-terminal amino acids, preferentially methionine, from peptides and arylamides.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-156814 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Methionine aminopeptidase 1 Chain: A
Molecule details ›
Chain: A
Length: 305 amino acids
Theoretical weight: 34.26 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P53582 (Residues: 81-384; Coverage: 79%)
Gene names: KIAA0094, METAP1
Sequence domains: Metallopeptidase family M24
Structure domains: Creatinase/methionine aminopeptidase superfamily

Ligands and Environments

3 bound ligands:
Ligand CO 3 x CO
Ligand K 1 x K
Ligand OVA 1 x OVA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P21
Unit cell:
a: 47.713Å b: 77.398Å c: 47.489Å
α: 90° β: 91.62° γ: 90°
R-values:
R R work R free
0.177 0.175 0.212
Expression system: Escherichia coli BL21(DE3)

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Citations

2 citation in other articles

Activities and metabolomics of Cordyceps gunnii under different culture conditions.
Qu et al. (2022)
1 more