SMTL ID : 5ypd.1

Mycobacterium Tuberculosis Methionine aminopeptidase type 1c (C105N mutant) in complex with Methionine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

monomer

Ligands

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

CO.1: 7 residues within 4Å: Chain A: D.176, H.239, T.270, E.272, E.303 Ligands: CO.2, MET.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.176, A:H.239, A:E.272, A:E.303, MET.5 CO.2: 5 residues within 4Å: Chain A: D.165, D.176, E.303 Ligands: CO.1, MET.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.165, A:D.165, A:D.176, A:E.303

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

NA.3: 4 residues within 4Å: Chain A: L.142, N.143, V.145, T.299 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.143, A:T.299

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 2 residues within 4Å: Chain A: R.234, D.235 Ligand excluded by PLIP

1 x MET: METHIONINE(Non-covalent)

MET.5: 15 residues within 4Å: Chain A: T.128, Y.131, F.134, N.139, D.165, T.167, D.176, H.239, F.245, H.246, E.272, W.289, E.303 Ligands: CO.1, CO.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.245 Hydrogen bonds: A:T.167 Water bridges: A:D.165, A:D.165, A:Q.301 Salt bridges: A:H.239, A:H.246

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: H.148, F.236, G.288, W.289, V.291 Ligands: GOL.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.289 GOL.7: 3 residues within 4Å: Chain A: G.288, W.289 Ligands: GOL.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.289

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bala, S.C. et al., Discovery of a new class of type 1 methionine aminopeptidases that have relaxed substrate specificity. Int.J.Biol.Macromol. (2019)

Release Date

2018-11-07

Peptides

Methionine aminopeptidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Methionine aminopeptidase

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