SMTL ID : 7oih.3 (3 other biounits)

Glycosylation in the crystal structure of neutrophil myeloperoxidase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA- MAN: 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.1: 7 residues within 4Å: Chain A: N.190, N.193, L.197, A.199, V.200, Q.202, Q.205 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.4: 6 residues within 4Å: Chain B: N.190, N.193, A.199, V.200, Q.202, Q.205 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.205 Water bridges: B:Q.202

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

NAG-NAG.2: 4 residues within 4Å: Chain A: N.226, A.229, W.370, L.374 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-MAN-MAN-FUC.3: 13 residues within 4Å: Chain A: R.315, N.318, S.320, V.321 Chain B: W.33, L.34, K.309, R.439, F.440, G.442, K.506 Ligands: NAG-NAG-BMA-MAN-MAN-FUC.6, NAG-NAG-BMA-MAN-MAN-FUC.6 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.506 Water bridges: A:S.320 Hydrophobic interactions: B:L.34, A:V.321 NAG-NAG-BMA-MAN-MAN-FUC.6: 14 residues within 4Å: Chain A: L.34, K.309, Y.310, R.439, F.440, G.442, K.506 Chain B: R.315, N.318, S.320, V.321, R.505 Ligands: NAG-NAG-BMA-MAN-MAN-FUC.3, NAG-NAG-BMA-MAN-MAN-FUC.3 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.506 Hydrophobic interactions: A:L.34, B:V.321 Water bridges: B:S.320

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.5: 4 residues within 4Å: Chain B: N.226, S.228, A.229, W.370 No protein-ligand interaction detected (PLIP)

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

CL.7: 5 residues within 4Å: Chain A: R.32, W.33, N.327, V.328, W.437 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: N.349, R.383, T.545 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: N.201, Q.202, F.214 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain A: Y.294, W.515 Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain B: R.32, W.33, N.327, V.328, W.437 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain B: Y.294, W.515 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain B: N.201, Q.202, F.214 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain B: N.396, N.458 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain A: R.324 Chain B: P.35, A.36, I.161 Ligand excluded by PLIP

2 x CA: CALCIUM ION(Non-covalent)

CA.10: 5 residues within 4Å: Chain A: D.97, T.169, F.171, D.173, S.175 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.169, A:T.169, A:F.171, A:D.173, A:S.175 CA.17: 5 residues within 4Å: Chain B: D.97, T.169, F.171, D.173, S.175 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.97, B:T.169, B:T.169, B:F.171, B:S.175

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.11: 23 residues within 4Å: Chain A: M.88, G.91, Q.92, D.95, D.99, F.100, T.101, R.240, E.243, M.244, T.330, F.333, R.334, G.336, H.337, I.340, F.366, L.407, F.408, L.418, L.421, R.425 Ligands: SCN.12 19 PLIP interactions: 18 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:Q.92, A:Q.92, A:E.243, A:F.333, A:F.333, A:R.334, A:I.340, A:F.366, A:L.407, A:F.408, A:L.418, A:L.418 Hydrogen bonds: A:D.99, A:T.101 Salt bridges: A:R.240, A:R.334, A:R.425 Metal complexes: A:H.337, H2O.2 HEM.19: 24 residues within 4Å: Chain B: M.88, G.91, Q.92, D.95, D.99, F.100, T.101, R.240, E.243, M.244, Y.297, T.330, F.333, R.334, Y.335, G.336, H.337, I.340, F.366, F.408, L.418, L.421, R.425 Ligands: SCN.20 21 PLIP interactions: 20 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: B:Q.92, B:Q.92, B:F.333, B:R.334, B:Y.335, B:I.340, B:F.366, B:F.408, B:L.418, B:L.418 Hydrogen bonds: B:D.99, B:D.99, B:T.101, B:T.101 Water bridges: B:R.240, B:T.330 Salt bridges: B:R.240, B:R.334, B:R.425 Metal complexes: B:H.337, H2O.12

2 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.12: 5 residues within 4Å: Chain A: Q.92, H.96, R.240, E.243 Ligands: HEM.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.92 SCN.20: 6 residues within 4Å: Chain B: H.96, R.240, E.243, F.408 Ligands: HEM.19, 8PR.21 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.92 Water bridges: B:R.240

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.14: 4 residues within 4Å: Chain A: D.6, R.512, F.513, V.520 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.512 PO4.24: 5 residues within 4Å: Chain B: R.295, A.530, Q.531, I.532, N.550 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.550 Salt bridges: B:R.295

1 x 8PR: Paroxetine(Non-covalent)

8PR.21: 7 residues within 4Å: Chain B: F.100, E.103, D.219, P.221, T.239, V.411 Ligands: SCN.20 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.100, B:P.221, B:V.411

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krawczyk, L. et al., Native glycosylation and binding of the antidepressant paroxetine in a low-resolution crystal structure of human myeloperoxidase. Acta Crystallogr D Struct Biol (2022)

Release Date

2022-08-24

Peptides

Myeloperoxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

Myeloperoxidase

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