SMTL ID : 6erc.2 (1 other biounit)

Peroxidase A from Dictyostelium discoideum (DdPoxA)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: S.306, E.354, N.355, D.357, Y.359 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.306, A:S.306, A:N.355, A:Y.359, H2O.2

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.2: 31 residues within 4Å: Chain A: N.73, M.74, G.76, Q.77, I.80, A.84, L.85, S.86, Y.116, R.213, E.216, N.217, Y.270, T.297, T.298, F.301, R.302, F.303, G.304, H.305, E.307, V.308, I.327, Y.331, L.364, L.368, F.369, L.379, R.382, N.383, R.386 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:N.73, A:Q.77, A:Q.77, A:E.216, A:F.301, A:F.301, A:R.302, A:Y.331, A:L.364, A:F.369, A:L.379 Hydrogen bonds: A:S.86, A:S.86, A:T.297, A:T.297 Salt bridges: A:R.213, A:R.302, A:R.302, A:R.382, A:R.386 Metal complexes: A:H.305

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

NAG.3: 3 residues within 4Å: Chain A: N.42, T.44, E.135 No protein-ligand interaction detected (PLIP)

1 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.4: 9 residues within 4Å: Chain A: Q.58, Q.59, T.60, H.61, P.310, E.354, I.361, S.362, D.363 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:H.61

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.5: 8 residues within 4Å: Chain A: D.57, Q.58, Q.59, T.60, I.62, Y.359, Q.418, R.422 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.59, A:I.62 Hydrogen bonds: A:Q.418

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

NA.6: 6 residues within 4Å: Chain A: N.82, M.83, G.147, Y.149, D.151, N.153 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.151, A:D.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nicolussi, A. et al., Secreted heme peroxidase from Dictyostelium discoideum: Insights into catalysis, structure, and biological role. J. Biol. Chem. (2018)

Release Date

2017-12-27

Peptides

Peroxinectin A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Peroxinectin A

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