SMTL ID : 6lzc.1

crystal structure of Human Methionine aminopeptidase (HsMetAP1b) in complex with KV-P2-4H-05

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 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, EYL.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.176, A:H.239, A:E.272, A:E.303, H2O.1 CO.2: 6 residues within 4Å: Chain A: D.165, T.167, D.176, E.303 Ligands: CO.1, EYL.3 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.165, A:D.165, A:E.303, H2O.1, EYL.3

1 x EYL: ~{N}-oxidanyl-1-(phenylmethyl)pyrrolo[2,3-b]pyridine-4-carboxamide(Non-covalent)

EYL.3: 15 residues within 4Å: Chain A: P.128, Y.131, F.134, H.148, D.165, T.167, D.176, H.239, F.245, H.246, E.272, E.303 Ligands: CO.1, CO.2, GOL.7 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.128 Hydrogen bonds: A:T.167 pi-Stacking: A:Y.131, A:F.245, A:W.289 pi-Cation interactions: A:H.148

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

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

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: R.42, P.43, H.113, H.116, L.117 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.42, A:P.43, A:H.113 GOL.6: 4 residues within 4Å: Chain A: A.99, G.100, H.326, S.329 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.99, A:S.329, A:S.329 Water bridges: A:R.319 GOL.7: 4 residues within 4Å: Chain A: H.148, Y.236, H.246 Ligands: EYL.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.246

1 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 1 residues within 4Å: Chain A: H.35 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.35, H2O.2, H2O.5, H2O.7, H2O.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bala, S. et al., Selective inhibition of Helicobacter pylori methionine aminopeptidase by azaindole hydroxamic acid derivatives: Design, synthesis, in vitro biochemical and structural studies. Bioorg.Chem. (2021)

Release Date

2021-02-24

Peptides

Methionine aminopeptidase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Methionine aminopeptidase 1

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