SMTL ID : 5yr4.1

Human methionine aminopeptidase type 1b (F309M mutant) in complex with TNP470

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

monomer

Ligands

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

CO.1: 4 residues within 4Å: Chain A: D.140, D.151, E.278 Ligands: CO.2 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.3 CO.2: 7 residues within 4Å: Chain A: D.151, H.214, T.245, E.247, E.278 Ligands: CO.1, TN4.7 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.3 CO.3: 2 residues within 4Å: Chain A: H.123 Ligands: TN4.7 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.123, H2O.6, H2O.6, H2O.6 CO.4: 3 residues within 4Å: Chain A: E.39, Y.106, H.221 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Y.106, A:H.221, H2O.7

1 x K: POTASSIUM ION(Non-covalent)

K.5: 5 residues within 4Å: Chain A: S.116, V.117, N.118, V.120, S.274 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.116, A:N.118, A:V.120, A:S.274, H2O.1

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 11 residues within 4Å: Chain A: L.7, T.83, T.115, S.116, V.117, V.120, G.124, I.125, P.126, D.127, W.260 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.83, A:T.115, A:V.117, A:I.125, A:D.127 Water bridges: A:I.125, A:D.127, A:D.127

1 x TN4: (1R,2S,3S,4R)-4-hydroxy-2-methoxy-4-methyl-3-[(2R,3R)-2-methyl-3-(3-methylbut-2-en-1-yl)oxiran-2-yl]cyclohexyl (chloroacetyl)carbamate(Covalent)

TN4.7: 15 residues within 4Å: Chain A: P.103, Y.106, F.109, C.114, H.123, S.210, Y.211, C.212, H.214, M.220, H.221, E.247, W.264 Ligands: CO.2, CO.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.103, A:Y.106, A:F.109, A:W.264 Hydrogen bonds: A:S.210, 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