SMTL ID : 9qe3.1

Structure of native leukocyte myeloperoxidase in complex with a truncated version of the Staphylococcal Peroxidase Inhibitor SPIN and selenocyanate at pH 5.5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

hetero-2-2-2-mer

Ligands

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.1: 18 residues within 4Å: Chain D: W.34, L.35 Chain E: N.205, S.207, V.208, R.392, K.393, D.396 Chain F: Y.197, R.326, F.327, C.328, G.329, C.385, T.389, K.393 Ligands: NAG-NAG-BMA-MAN-FUC.2, NAG-NAG-BMA-MAN-FUC.2 4 PLIP interactions: 1 interactions with chain E, 2 interactions with chain F, 1 interactions with chain D Hydrophobic interactions: E:V.208, E:K.393, D:L.35 Water bridges: E:R.392, E:S.207 Hydrogen bonds: F:K.393, F:R.326, F:F.327 NAG-NAG-BMA-MAN-FUC.2: 18 residues within 4Å: Chain C: W.34, L.35 Chain E: Y.197, R.326, F.327, C.328, G.329, C.385, T.389, K.393 Chain F: N.205, S.207, V.208, R.392, K.393, D.396 Ligands: NAG-NAG-BMA-MAN-FUC.1, NAG-NAG-BMA-MAN-FUC.1 4 PLIP interactions: 1 interactions with chain F, 2 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: F:V.208, C:L.35 Hydrogen bonds: F:R.392, E:K.393, E:R.326, E:F.327 Water bridges: F:S.207

32 x SEK: SELENOCYANATE ION(Non-covalent)(Non-functional Binders)

SEK.3: 7 residues within 4Å: Chain C: R.33, P.36, A.37 Chain D: S.21, L.24 Chain E: I.48 Chain F: R.211 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:A.37, F:R.211 SEK.4: 1 residues within 4Å: Chain C: R.72 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.72 SEK.5: 3 residues within 4Å: Chain C: R.72, F.73, P.74 No protein-ligand interaction detected (PLIP) SEK.7: 10 residues within 4Å: Chain C: V.32, R.33, W.34, L.35 Chain E: A.213, N.214, V.215, L.318, P.319, W.324 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:N.214, E:V.215, C:W.34 SEK.8: 10 residues within 4Å: Chain D: V.32, R.33, W.34, L.35 Chain F: A.213, N.214, V.215, L.318, P.319, W.324 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain D Hydrogen bonds: F:N.214, F:V.215, D:W.34 SEK.10: 3 residues within 4Å: Chain D: E.83, R.84 Chain F: K.376 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.84, D:R.84 SEK.11: 5 residues within 4Å: Chain E: I.178, Y.181, R.182, W.401, W.402 No protein-ligand interaction detected (PLIP) SEK.12: 4 residues within 4Å: Chain E: E.4, T.5, M.299, R.300 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.300 SEK.13: 6 residues within 4Å: Chain E: P.331, Q.332, P.333, Q.338, T.341, V.342 No protein-ligand interaction detected (PLIP) SEK.14: 5 residues within 4Å: Chain E: R.127, E.130, F.254, F.295 Ligands: HEM.6 No protein-ligand interaction detected (PLIP) SEK.15: 6 residues within 4Å: Chain C: L.45, W.49 Chain E: P.11, P.12, R.36, R.49 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.49, E:R.49 SEK.16: 6 residues within 4Å: Chain E: Q.282, N.283, N.345, K.347, L.348, K.351 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:K.351 SEK.17: 7 residues within 4Å: Chain A: E.5, H.6 Chain E: N.88, Q.89, R.90, P.100, F.101 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:Q.89, E:R.90, E:R.90, A:E.5 SEK.18: 4 residues within 4Å: Chain E: R.96, A.97, R.143, N.428 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.96 SEK.19: 4 residues within 4Å: Chain C: Y.9 Chain E: E.162, R.163, Q.166 No protein-ligand interaction detected (PLIP) SEK.20: 5 residues within 4Å: Chain E: N.244, R.246, V.247, P.248, R.258 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.244 SEK.21: 3 residues within 4Å: Chain E: P.186, P.191, M.194 No protein-ligand interaction detected (PLIP) SEK.22: 8 residues within 4Å: Chain E: T.112, N.113, R.251, W.257, R.258, Q.297 Ligands: SEK.23, NAG.25 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.258, E:Q.297 Water bridges: E:W.257 SEK.23: 2 residues within 4Å: Chain E: Q.297 Ligands: SEK.22 No protein-ligand interaction detected (PLIP) SEK.27: 7 residues within 4Å: Chain C: S.21, L.24 Chain D: R.33, P.36, A.37 Chain E: R.211 Chain F: I.48 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 1 interactions with chain E Hydrogen bonds: C:S.21, D:A.37, E:R.211 Water bridges: C:L.24 SEK.28: 7 residues within 4Å: Chain D: A.30 Chain E: C.41, T.47 Chain F: A.40, C.41, T.47, N.50 1 PLIP interactions: 1 interactions with chain F Water bridges: F:T.47 SEK.29: 6 residues within 4Å: Chain F: I.178, Y.181, R.182, R.395, W.401, W.402 No protein-ligand interaction detected (PLIP) SEK.30: 5 residues within 4Å: Chain F: P.331, P.333, Q.338, T.341, V.342 1 PLIP interactions: 1 interactions with chain F Water bridges: F:T.341 SEK.31: 7 residues within 4Å: Chain D: I.70 Chain F: Q.282, N.283, N.345, K.347, L.348, K.351 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:K.351 SEK.32: 7 residues within 4Å: Chain D: Q.93, H.97 Chain F: R.127, E.130, F.254, F.295 Ligands: HEM.9 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.93, D:H.97 SEK.33: 6 residues within 4Å: Chain F: R.325, P.331, V.342, E.371, P.372, P.381 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:R.325 SEK.34: 1 residues within 4Å: Chain F: R.375 No protein-ligand interaction detected (PLIP) SEK.35: 5 residues within 4Å: Chain D: W.49 Chain F: P.11, P.12, R.36, R.49 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.49, F:R.49 SEK.36: 4 residues within 4Å: Chain D: E.69 Chain F: K.351, E.354, Q.355 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:E.354 SEK.37: 5 residues within 4Å: Chain D: K.8, Y.9 Chain F: E.162, R.163, Q.166 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.8 SEK.38: 5 residues within 4Å: Chain F: F.232, L.234, P.240, P.245, R.246 No protein-ligand interaction detected (PLIP) SEK.39: 7 residues within 4Å: Chain B: E.5, H.6 Chain F: N.88, Q.89, R.90, P.100, F.101 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Q.89, F:R.90

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.6: 29 residues within 4Å: Chain C: F.31, M.89, G.92, Q.93, D.96, D.100, F.101, T.102 Chain E: F.34, R.127, E.130, M.131, Y.184, T.217, F.220, R.221, Y.222, G.223, H.224, L.226, I.227, F.253, L.294, F.295, L.305, L.308, N.309, R.312 Ligands: SEK.14 25 PLIP interactions: 19 interactions with chain E, 5 interactions with chain C, 1 Ligand-Water interactions, Hydrophobic interactions: E:E.130, E:F.220, E:R.221, E:I.227, E:F.253, E:L.294, E:L.294, E:F.295, E:F.295, E:L.305, E:L.305, C:Q.93, C:Q.93, C:D.96 Water bridges: E:R.221, E:R.221, E:R.221, E:R.221 Salt bridges: E:R.127, E:R.221, E:R.312 Metal complexes: E:H.224, H2O.3 Hydrogen bonds: C:D.100, C:T.102 HEM.9: 29 residues within 4Å: Chain D: F.31, M.89, G.92, Q.93, D.96, D.100, F.101, T.102 Chain F: F.34, R.127, E.130, M.131, Y.184, T.217, F.220, R.221, Y.222, G.223, H.224, L.226, I.227, F.253, L.294, F.295, L.305, L.308, N.309, R.312 Ligands: SEK.32 24 PLIP interactions: 4 interactions with chain D, 19 interactions with chain F, 1 Ligand-Water interactions, Hydrophobic interactions: D:Q.93, D:Q.93, F:E.130, F:M.131, F:F.220, F:R.221, F:Y.222, F:I.227, F:F.253, F:F.295, F:L.305, F:L.305 Hydrogen bonds: D:D.100, D:T.102 Water bridges: F:R.221, F:R.221, F:R.221, F:R.221, F:R.312 Salt bridges: F:R.127, F:R.221, F:R.312 Metal complexes: F:H.224, H2O.4

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

NAG.24: 10 residues within 4Å: Chain A: H.6, Y.10 Chain E: N.77, S.79, N.80, L.82, L.84, A.86, V.87, Q.89 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:N.77, E:V.87 Hydrogen bonds: E:N.80, E:Q.89 Water bridges: E:N.77, A:S.9 NAG.25: 6 residues within 4Å: Chain E: N.113, S.115, A.116, W.257, L.261 Ligands: SEK.22 No protein-ligand interaction detected (PLIP) NAG.40: 11 residues within 4Å: Chain B: H.6, S.9, Y.10 Chain F: N.77, S.79, N.80, L.82, L.84, A.86, V.87, Q.89 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain B Hydrophobic interactions: F:A.86, B:Y.10 Hydrogen bonds: F:N.80, F:V.87, F:Q.89 NAG.41: 6 residues within 4Å: Chain F: N.113, S.115, A.116, W.257, R.258, L.261 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:S.115

2 x CA: CALCIUM ION(Non-covalent)

CA.26: 5 residues within 4Å: Chain C: D.98 Chain E: T.56, F.58, D.60, S.62 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain C Metal complexes: E:T.56, E:F.58, E:D.60, E:S.62, C:D.98 CA.42: 5 residues within 4Å: Chain D: D.98 Chain F: T.56, F.58, D.60, S.62 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain D Metal complexes: F:T.56, F:T.56, F:F.58, F:S.62, D: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 inhibitor SPIN: AB
Myeloperoxidase light chain: CD
Myeloperoxidase heavy chain: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
A

D
C

E
B

F
D

Myeloperoxidase inhibitor SPIN

Myeloperoxidase light chain

Myeloperoxidase heavy chain

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