SMTL ID : 9qga.1

Structure of native leukocyte myeloperoxidase in complex with a truncated version of the Staphylococcal Peroxidase Inhibitor SPIN and bromide at pH 7.5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

hetero-2-2-2-mer

Ligands

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.1: 6 residues within 4Å: Chain E: N.113, S.115, A.116, W.257, L.261 Ligands: BR.31 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN- FUC: 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-FUC.2: 13 residues within 4Å: Chain B: W.34, L.35 Chain E: N.205, S.207, V.208, R.392 Chain F: Y.197, R.326, F.327, G.329, K.393 Ligands: NAG-NAG-BMA-MAN-FUC.3, NAG-NAG-BMA-MAN-FUC.3 3 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E, 1 interactions with chain B Hydrophobic interactions: F:R.326, F:F.327, E:V.208 Water bridges: E:S.207, E:D.209, F:K.196, F:K.196 Hydrogen bonds: B:W.34, F:K.393 NAG-NAG-BMA-MAN-FUC.3: 15 residues within 4Å: Chain A: W.34, L.35 Chain E: R.326, F.327, G.329, K.393 Chain F: R.202, N.205, S.207, V.208, R.392, K.393 Ligands: NAG-NAG-BMA-MAN-FUC.2, NAG-NAG-BMA-MAN-FUC.2, BR.49 6 PLIP interactions: 4 interactions with chain F, 1 interactions with chain A, 1 interactions with chain E Water bridges: F:S.207, F:R.392 Hydrophobic interactions: A:L.35, F:V.208, F:R.392 Hydrogen bonds: F:K.393, E:K.393, A:W.34

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.4: 21 residues within 4Å: Chain A: M.89, G.92, Q.93, D.96, D.100, F.101, T.102 Chain E: R.127, E.130, M.131, T.217, F.220, R.221, G.223, H.224, I.227, F.253, F.295, L.305, L.308, R.312 19 PLIP interactions: 14 interactions with chain E, 5 interactions with chain A, Hydrophobic interactions: E:E.130, E:R.221, E:F.253, E:F.295, E:L.305, E:L.305, A:Q.93, A:Q.93 Water bridges: E:R.221, E:R.221, E:R.312, E:R.312, A:T.102 Salt bridges: E:R.127, E:R.221, E:R.312 Metal complexes: E:H.224 Hydrogen bonds: A:D.100, A:T.102 HEM.9: 21 residues within 4Å: Chain B: M.89, G.92, Q.93, D.96, D.100, F.101, T.102 Chain F: R.127, E.130, M.131, Y.184, T.217, F.220, R.221, G.223, H.224, I.227, F.253, F.295, L.305, R.312 22 PLIP interactions: 16 interactions with chain F, 5 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: F:E.130, F:M.131, F:R.221, F:I.227, F:F.253, F:F.295, F:L.305, F:L.305, B:Q.93, B:Q.93 Water bridges: F:R.221, F:R.221, F:R.221, F:R.221 Salt bridges: F:R.127, F:R.221, F:R.312 Metal complexes: F:H.224, H2O.5 Hydrogen bonds: B:D.100, B:T.102, B:T.102

46 x BR: BROMIDE ION(Non-covalent)

BR.5: 5 residues within 4Å: Chain A: R.33, W.34 Chain E: N.214, V.215, W.324 Ligand excluded by PLIP BR.6: 3 residues within 4Å: Chain A: R.72, F.73, P.74 Ligand excluded by PLIP BR.7: 3 residues within 4Å: Chain A: E.83, R.84 Chain E: K.376 Ligand excluded by PLIP BR.8: 3 residues within 4Å: Chain A: P.36, A.37 Chain E: I.48 Ligand excluded by PLIP BR.10: 5 residues within 4Å: Chain B: R.33, W.34 Chain F: N.214, V.215, W.324 Ligand excluded by PLIP BR.11: 3 residues within 4Å: Chain B: R.72, F.73, P.74 Ligand excluded by PLIP BR.12: 3 residues within 4Å: Chain B: P.36, A.37 Chain F: I.48 Ligand excluded by PLIP BR.14: 4 residues within 4Å: Chain E: R.270, I.431, T.432, T.433 Ligand excluded by PLIP BR.15: 2 residues within 4Å: Chain E: P.12, R.49 Ligand excluded by PLIP BR.16: 3 residues within 4Å: Chain E: N.345, K.347, K.351 Ligand excluded by PLIP BR.17: 3 residues within 4Å: Chain E: R.96, A.97, R.143 Ligand excluded by PLIP BR.18: 2 residues within 4Å: Chain E: Y.181, W.402 Ligand excluded by PLIP BR.19: 4 residues within 4Å: Chain E: T.192, A.193, K.196, K.374 Ligand excluded by PLIP BR.20: 1 residues within 4Å: Chain E: P.333 Ligand excluded by PLIP BR.21: 1 residues within 4Å: Chain E: R.300 Ligand excluded by PLIP BR.22: 2 residues within 4Å: Chain E: R.325, P.381 Ligand excluded by PLIP BR.23: 3 residues within 4Å: Chain B: R.20 Chain E: R.326, N.360 Ligand excluded by PLIP BR.24: 4 residues within 4Å: Chain E: P.422, N.437, N.438, I.439 Ligand excluded by PLIP BR.25: 2 residues within 4Å: Chain E: R.127, E.130 Ligand excluded by PLIP BR.26: 4 residues within 4Å: Chain E: S.207, V.208, D.209, K.393 Ligand excluded by PLIP BR.27: 3 residues within 4Å: Chain E: I.25, K.26, N.27 Ligand excluded by PLIP BR.28: 3 residues within 4Å: Chain E: R.281, Q.282, N.283 Ligand excluded by PLIP BR.29: 1 residues within 4Å: Chain E: P.191 Ligand excluded by PLIP BR.30: 6 residues within 4Å: Chain C: E.5, H.6 Chain E: N.88, Q.89, P.100, F.101 Ligand excluded by PLIP BR.31: 3 residues within 4Å: Chain E: T.112, Q.297 Ligands: NAG-NAG.1 Ligand excluded by PLIP BR.32: 1 residues within 4Å: Chain E: P.248 Ligand excluded by PLIP BR.33: 3 residues within 4Å: Chain E: K.436, N.437, L.455 Ligand excluded by PLIP BR.34: 2 residues within 4Å: Chain A: Y.9 Chain E: R.163 Ligand excluded by PLIP BR.38: 5 residues within 4Å: Chain F: N.236, R.270, I.431, T.432, T.433 Ligand excluded by PLIP BR.39: 2 residues within 4Å: Chain F: P.12, R.49 Ligand excluded by PLIP BR.40: 2 residues within 4Å: Chain F: N.283, N.345 Ligand excluded by PLIP BR.41: 3 residues within 4Å: Chain F: R.96, A.97, R.143 Ligand excluded by PLIP BR.42: 2 residues within 4Å: Chain F: Y.181, W.402 Ligand excluded by PLIP BR.43: 1 residues within 4Å: Chain F: P.331 Ligand excluded by PLIP BR.44: 1 residues within 4Å: Chain F: R.325 Ligand excluded by PLIP BR.45: 2 residues within 4Å: Chain B: R.84 Chain F: K.376 Ligand excluded by PLIP BR.46: 3 residues within 4Å: Chain A: R.20 Chain F: R.326, N.360 Ligand excluded by PLIP BR.47: 4 residues within 4Å: Chain F: P.422, N.437, N.438, I.439 Ligand excluded by PLIP BR.48: 2 residues within 4Å: Chain F: R.127, E.130 Ligand excluded by PLIP BR.49: 5 residues within 4Å: Chain F: S.207, V.208, D.209, K.393 Ligands: NAG-NAG-BMA-MAN-FUC.3 Ligand excluded by PLIP BR.50: 2 residues within 4Å: Chain F: P.186, P.191 Ligand excluded by PLIP BR.51: 6 residues within 4Å: Chain D: E.5, H.6 Chain F: N.88, Q.89, P.100, F.101 Ligand excluded by PLIP BR.52: 1 residues within 4Å: Chain F: K.374 Ligand excluded by PLIP BR.53: 2 residues within 4Å: Chain F: W.257, Q.297 Ligand excluded by PLIP BR.54: 3 residues within 4Å: Chain B: Y.9 Chain F: E.162, R.163 Ligand excluded by PLIP BR.55: 1 residues within 4Å: Chain F: R.375 Ligand excluded by PLIP

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

NAG.13: 10 residues within 4Å: Chain C: H.6, S.9, Y.10 Chain E: N.77, S.79, N.80, L.84, A.86, V.87, Q.89 8 PLIP interactions: 2 interactions with chain C, 6 interactions with chain E Hydrophobic interactions: C:Y.10 Water bridges: C:S.9, E:N.77, E:S.79 Hydrogen bonds: E:N.80, E:V.87, E:Q.89, E:Q.89 NAG.36: 2 residues within 4Å: Chain F: N.113, W.257 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.113 NAG.37: 9 residues within 4Å: Chain D: H.6, S.9 Chain F: N.77, S.79, N.80, L.84, A.86, V.87, Q.89 8 PLIP interactions: 7 interactions with chain F, 1 interactions with chain D Hydrophobic interactions: F:A.86, D:H.6 Hydrogen bonds: F:N.80, F:V.87, F:Q.89, F:Q.89 Water bridges: F:N.77, F:N.77

2 x CA: CALCIUM ION(Non-covalent)

CA.35: 5 residues within 4Å: Chain A: D.98 Chain E: T.56, F.58, D.60, S.62 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain E Metal complexes: A:D.98, A:D.98, E:T.56, E:F.58, E:S.62 CA.56: 5 residues within 4Å: Chain B: D.98 Chain F: T.56, F.58, D.60, S.62 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain B Metal complexes: F:T.56, F:F.58, F:D.60, F:S.62, B:D.98

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leitgeb, U. et al., Halide binding by myeloperoxidase is regulated by access channel dynamics and charge interactions. Int.J.Biol.Macromol. (2025)

Release Date

2025-10-15

Peptides

Myeloperoxidase light chain: AB
Myeloperoxidase inhibitor SPIN: CD
Myeloperoxidase heavy chain: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

D
F

E
B

F
D

Myeloperoxidase light chain

Myeloperoxidase inhibitor SPIN

Myeloperoxidase heavy chain

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