SMTL ID : 5yr5.1

Human methionine aminopeptidase type 1b (F309L mutant) in complex with Ovalicin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

3 x CO: COBALT (II) ION(Non-covalent)

CO.1: 7 residues within 4Å: Chain A: D.151, H.214, T.245, E.247, E.278 Ligands: CO.2, OVA.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.151, A:H.214, A:E.247, A:E.278, H2O.2 CO.2: 4 residues within 4Å: Chain A: D.140, D.151, E.278 Ligands: CO.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.140, A:D.151, A:E.278, H2O.2, H2O.2 CO.3: 4 residues within 4Å: Chain A: E.39, Y.106, Y.107, H.221 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.39, A:Y.106, A:H.221, H2O.8, H2O.8

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 4 residues within 4Å: Chain A: V.117, N.118, V.120, S.274 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.118, A:S.274

1 x OVA: 3,4-DIHYDROXY-2-METHOXY-4-METHYL-3-[2-METHYL-3-(3-METHYL-BUT-2-ENYL) -OXIRANYL]-CYCLOHEXANONE(Covalent)

OVA.5: 11 residues within 4Å: Chain A: P.103, Y.106, H.123, Y.211, C.212, H.214, L.220, H.221, E.247, W.264 Ligands: CO.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.103, A:Y.106, A:Y.106, A:Y.211, A:L.220, A:H.221, A:W.264 Hydrogen bonds: A:C.212

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pillalamarri, V. et al., Discovery of natural product ovalicin sensitive type 1 methionine aminopeptidases: molecular and structural basis. Biochem. J. (2019)

Release Date

2018-11-14

Peptides

Methionine aminopeptidase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Methionine aminopeptidase 1

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