SMTL ID : 5yr6.1

Human methionine aminopeptidase type 1b (F309L mutant) in complex with TNP470

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

2 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, TN4.4 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.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.3

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

NA.3: 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:S.116, A:S.274

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)

TN4.4: 13 residues within 4Å: Chain A: P.103, Y.106, F.109, C.114, H.123, S.210, Y.211, C.212, H.214, H.221, E.247, W.264 Ligands: CO.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.103, A:Y.106, 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

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