SMTL ID : 7oih.1 (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

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.1: 5 residues within 4Å: Chain B: N.226, S.228, A.229, W.370, L.374 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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-MAN.2: 7 residues within 4Å: Chain A: N.190, N.193, L.197, A.199, V.200, Q.202, Q.205 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.205, A:Q.205, A:Q.205

1 x NAG- NAG- BMA- MAN- NAG- MAN- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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-NAG-MAN-FUC.3: 16 residues within 4Å: Chain A: N.318, S.320, V.321, K.506 Chain B: W.33, L.34, K.309, Y.310, R.439, F.440, G.442, K.506 Ligands: NAG-NAG-BMA-MAN-MAN-FUC.5, NAG-NAG-BMA-MAN-MAN-FUC.5, NAG-NAG-BMA-MAN-MAN-FUC.5, NAG-NAG-BMA-MAN-MAN-FUC.5 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.440, A:V.321 Hydrogen bonds: B:K.309, A:K.506

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.4: 6 residues within 4Å: Chain B: N.190, N.193, L.197, A.199, V.200, Q.202 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.202 NAG-NAG.6: 5 residues within 4Å: Chain A: N.226, S.228, A.229, W.370, L.374 No protein-ligand interaction detected (PLIP)

1 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.5: 16 residues within 4Å: Chain A: W.33, 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-NAG-MAN-FUC.3, NAG-NAG-BMA-MAN-NAG-MAN-FUC.3, NAG-NAG-BMA-MAN-NAG-MAN-FUC.3 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.34, B:V.321 Water bridges: B:S.320, B:R.505, B:R.505 Hydrogen bonds: A:W.33, A:K.506

10 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: 5 residues within 4Å: Chain A: N.349, R.383, I.544, T.545, T.546 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: N.201, Q.202, F.214 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain A: N.396, N.458 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain A: Y.294, W.515 Ligand excluded by PLIP CL.17: 5 residues within 4Å: Chain B: R.32, W.33, N.327, V.328, W.437 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain B: Y.294, W.515 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain B: N.201, Q.202, F.214 Ligand excluded by PLIP CL.26: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.27: 4 residues within 4Å: Chain B: Q.395, N.396, N.458, L.461 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.20: 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: 24 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, 8PR.13 21 PLIP interactions: 20 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:Q.92, A:Q.92, A:E.243, A:R.334, A:F.366, A:L.407, A:F.408, A:L.418, A:L.418 Hydrogen bonds: A:D.99, A:T.101 Water bridges: A:T.101, A:R.334, A:R.334, A:R.334, A:R.425 Salt bridges: A:R.240, A:R.334, A:R.425 Metal complexes: A:H.337, H2O.1 HEM.23: 22 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, T.330, F.333, R.334, G.336, H.337, I.340, F.366, F.408, L.418, L.421, R.425 Ligands: SCN.24 21 PLIP interactions: 20 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: B:Q.92, B:Q.92, B:E.243, B:F.333, B:R.334, 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.334, B:R.334 Salt bridges: B:R.240, B:R.334, B:R.425 Metal complexes: B:H.337, H2O.15

3 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.24: 5 residues within 4Å: Chain B: Q.92, H.96, R.240, E.243 Ligands: HEM.23 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.92 Water bridges: B:R.240 SCN.25: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x 8PR: Paroxetine(Non-covalent)

8PR.13: 8 residues within 4Å: Chain A: F.100, E.103, E.117, P.221, T.239, F.367, V.411 Ligands: HEM.11 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.100, A:P.221, A:F.367, A:V.411 Water bridges: A:E.103, A:E.103

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

PO4.16: 6 residues within 4Å: Chain A: R.295, A.530, Q.531, I.532, S.533, N.550 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.530, A:N.550 Salt bridges: A:R.295 PO4.28: 4 residues within 4Å: Chain B: R.512, F.513, N.517, V.520 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.517, B:E.518 Salt bridges: B:R.512 PO4.29: 2 residues within 4Å: Chain B: P.221, M.412 No protein-ligand interaction detected (PLIP)

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

NAG.21: 2 residues within 4Å: Chain B: G.156, N.158 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.156, B:N.158 Water bridges: B:N.158 NAG.22: 2 residues within 4Å: Chain B: F.562, N.564 No protein-ligand interaction detected (PLIP)

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
A

B
B

Myeloperoxidase

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