SMTL ID : 7oih.4 (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- 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.1: 15 residues within 4Å: Chain A: N.318, S.320, V.321, R.505 Chain B: W.33, L.34, K.309, Y.310, R.439, F.440, G.442, K.506 Ligands: NAG-NAG-BMA-MAN-NAG-MAN-FUC.2, NAG-NAG-BMA-MAN-NAG-MAN-FUC.2, NAG-NAG-BMA-MAN-NAG-MAN-FUC.2 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.321, B:F.440 Hydrogen bonds: A:R.505, B:K.309 Water bridges: A:K.506 NAG-NAG-BMA-MAN-NAG-MAN-FUC.2: 17 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.1, NAG-NAG-BMA-MAN-NAG-MAN-FUC.1, NAG-NAG-BMA-MAN-NAG-MAN-FUC.1, NAG-NAG-BMA-MAN-NAG-MAN-FUC.1 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.321, A:F.440 Water bridges: B:R.505, B:R.505, A:K.309, A:K.309 Hydrogen bonds: A:K.309

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.3: 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.202

2 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.4: 4 residues within 4Å: Chain A: N.226, A.229, W.370, L.374 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 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

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.5: 1 residues within 4Å: Chain B: N.158 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain B: N.226, S.228, A.229, W.370, L.374 No protein-ligand interaction detected (PLIP)

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

CL.8: 2 residues within 4Å: Chain A: Y.294, W.515 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain A: R.32, W.33, N.327, V.328, W.437 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: N.349, R.383, T.545 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain A: N.201, Q.202, R.203, F.214 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain A: N.396, N.458 Ligand excluded by PLIP CL.18: 5 residues within 4Å: Chain B: R.32, W.33, N.327, V.328, W.437 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain B: N.201, Q.202, F.214 Ligand excluded by PLIP CL.20: 1 residues within 4Å: Chain B: W.515 Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain B: N.396, N.458 Ligand excluded by PLIP

2 x CA: CALCIUM ION(Non-covalent)

CA.12: 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:D.97, A:D.97, A:T.169, A:F.171, A:S.175 CA.21: 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:F.171, B:D.173, B:S.175

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.13: 22 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, F.408, L.418, L.421, R.425 Ligands: SCN.14 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:I.340, A:F.366, A:F.408, A:L.418, A:L.418 Hydrogen bonds: A:D.99, A:D.99, A:T.101, A:T.101 Water bridges: A:R.334, A:R.334, A:R.334 Salt bridges: A:R.240, A:R.334, A:R.425 Metal complexes: A:H.337, H2O.1 HEM.22: 23 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.23, 8PR.24 17 PLIP interactions: 16 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: B:Q.92, B:Q.92, B:E.243, B:R.334, B:F.366, B:F.408, B:L.418, B:L.418 Hydrogen bonds: B:D.99, 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.13

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

SCN.14: 5 residues within 4Å: Chain A: Q.92, H.96, R.240, E.243 Ligands: HEM.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.92 Water bridges: A:R.240 SCN.23: 6 residues within 4Å: Chain B: Q.92, H.96, R.240, E.243 Ligands: HEM.22, 8PR.24 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.92

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

PO4.16: 5 residues within 4Å: Chain A: D.6, R.512, F.513, G.519, V.520 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.519 Salt bridges: A:R.512 PO4.17: 3 residues within 4Å: Chain A: P.304, R.488, K.489 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.488, A:K.489 PO4.26: 5 residues within 4Å: Chain B: R.295, A.530, Q.531, I.532, N.550 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.531, B:N.550 Salt bridges: B:R.295 PO4.27: 6 residues within 4Å: Chain B: K.7, E.280, K.283, V.520, Q.525, W.576 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:V.520, B:Q.525, B:W.576 Salt bridges: B:K.7, B:K.283

1 x 8PR: Paroxetine(Non-covalent)

8PR.24: 9 residues within 4Å: Chain B: F.100, E.103, D.219, P.221, T.239, V.411, M.412 Ligands: HEM.22, SCN.23 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
G

B
H

Myeloperoxidase

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