SMTL ID : 6bmt.1

Crystal Structure of a Recombinant form of Human Myeloperoxidase Bound to an Inhibitor from Staphylococcus delphini

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-1-1-mer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.262, T.334, F.336, D.338, S.340 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.262, A:T.334, A:F.336, A:D.338, A:S.340

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.2: 24 residues within 4Å: Chain A: M.253, G.256, Q.257, D.260, D.264, F.265, T.266, R.405, E.408, M.409, T.495, F.498, R.499, G.501, H.502, I.505, F.531, L.572, F.573, L.583, L.586, R.590 Chain B: Q.37, N.38 19 PLIP interactions: 17 interactions with chain A, 2 interactions with chain B, Hydrophobic interactions: A:Q.257, A:Q.257, A:M.409, A:F.498, A:R.499, A:I.505, A:F.531, A:L.572, A:F.573, A:L.583, A:L.583 Hydrogen bonds: A:D.264, A:T.266, B:N.38, B:N.38 Salt bridges: A:R.405, A:R.499, A:R.590 Metal complexes: A:H.502

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

CL.3: 6 residues within 4Å: Chain A: V.196, R.197, W.198, N.492, V.493, W.602 Ligand excluded by PLIP

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.4: 1 residues within 4Å: Chain A: N.483 No protein-ligand interaction detected (PLIP) NAG.5: 7 residues within 4Å: Chain A: N.355, S.357, N.358, L.362, A.364, V.365, Q.367 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.358, A:V.365, A:Q.367, A:Q.367, A:Q.367 NAG.6: 4 residues within 4Å: Chain A: N.391, S.393, A.394, W.535 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.393

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ploscariu, N.T. et al., Identification and structural characterization of a novel myeloperoxidase inhibitor from Staphylococcus delphini. Arch. Biochem. Biophys. (2018)

Release Date

2018-01-03

Peptides

Myeloperoxidase: A
Hypothetical Protein: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Myeloperoxidase

Hypothetical Protein