SMTL ID : 5mfa.1

Crystal structure of human promyeloperoxidase (proMPO)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

monomer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: N.343, S.345, A.346, W.487, L.491 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.435, S.437 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.3: 11 residues within 4Å: Chain A: N.307, S.309, N.310, L.312, L.314, A.316, V.317, Q.319, R.320, F.321, Q.322 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.322, A:Q.322

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

NAG.4: 3 residues within 4Å: Chain A: G.273, S.274, N.275 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.273, A:N.275 NAG.5: 4 residues within 4Å: Chain A: T.662, T.663, N.681, S.683 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.681, A:S.683

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.6: 28 residues within 4Å: Chain A: F.147, M.205, Q.206, G.208, Q.209, D.212, D.216, F.217, T.218, R.357, E.360, M.361, Y.414, T.447, F.450, R.451, Y.452, G.453, H.454, L.456, I.457, F.483, L.524, F.525, L.535, L.538, N.539, R.542 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:Q.209, A:Q.209, A:E.360, A:M.361, A:R.451, A:I.457, A:F.483, A:L.524, A:F.525, A:L.535, A:L.535 Hydrogen bonds: A:D.216, A:T.218, A:T.218 Water bridges: A:R.451, A:R.451, A:R.451, A:R.451 Salt bridges: A:R.357, A:R.451, A:R.542 Metal complexes: A:H.454

1 x CA: CALCIUM ION(Non-covalent)

CA.7: 6 residues within 4Å: Chain A: D.214, L.215, T.286, F.288, D.290, S.292 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.214, A:D.214, A:T.286, A:F.288, A:S.292

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

CL.8: 8 residues within 4Å: Chain A: R.149, W.150, L.151, A.443, N.444, V.445, L.548, W.554 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: N.513, N.575, K.577 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: P.241, P.242, R.266, R.279 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain A: N.318, Q.319, P.330, F.331 Ligand excluded by PLIP CL.12: 6 residues within 4Å: Chain A: N.466, Y.468, R.500, I.661, T.662, T.663 Ligand excluded by PLIP

5 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.13: 4 residues within 4Å: Chain A: K.426, Y.427, R.622 Ligands: PEG.16 6 PLIP interactions: 6 interactions with chain A Water bridges: A:K.426, A:Y.427, A:R.622, A:R.622, A:R.622, A:R.622 PEG.14: 7 residues within 4Å: Chain A: P.561, Q.562, P.563, Q.568, T.571, V.572 Ligands: PEG.15 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Q.568, A:Q.568, A:T.571 PEG.15: 2 residues within 4Å: Chain A: Q.568 Ligands: PEG.14 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.568, A:Q.568 PEG.16: 6 residues within 4Å: Chain A: Y.427, F.557, C.558, C.615, T.619 Ligands: PEG.13 4 PLIP interactions: 4 interactions with chain A Water bridges: A:Y.427, A:R.622, A:R.622, A:R.622 PEG.17: 6 residues within 4Å: Chain A: R.344, E.526, Q.527, V.528, M.529, R.530 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.344 Water bridges: A:R.344

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.18: 5 residues within 4Å: Chain A: P.338, F.484, F.525, V.528, M.529 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.220, A:E.234, A:V.528

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grishkovskaya, I. et al., Structure of human promyeloperoxidase (proMPO) and the role of the propeptide in processing and maturation. J. Biol. Chem. (2017)

Release Date

2017-04-05

Peptides

Myeloperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Myeloperoxidase