SMTL ID : 9qex.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-2-2-2-mer

Ligands

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.1: 6 residues within 4Å: Chain A: N.113, S.115, A.116, P.243, W.257, L.261 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 7 residues within 4Å: Chain B: N.113, S.115, A.116, N.244, W.257, R.258, L.261 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.2: 20 residues within 4Å: Chain A: N.205, S.207, V.208, R.392, K.393, D.396 Chain B: K.196, Y.197, R.326, F.327, C.328, G.329, C.385, T.389, K.393 Chain F: W.34, L.35 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 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 interactions with chain F Water bridges: A:S.207, B:C.328, B:T.389 Hydrogen bonds: B:F.327, A:R.392, B:K.393 Hydrophobic interactions: F:L.35, A:V.208

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: 20 residues within 4Å: Chain A: K.196, Y.197, R.326, F.327, C.328, G.329, C.385, T.389, K.393 Chain B: N.205, S.207, V.208, R.392, K.393, D.396 Chain E: W.34, L.35 Ligands: NAG-NAG-BMA-MAN-MAN-FUC.2, NAG-NAG-BMA-MAN-MAN-FUC.2, NAG-NAG-BMA-MAN-MAN-FUC.2 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Water bridges: A:C.328, B:R.392 Hydrophobic interactions: B:V.208 Hydrogen bonds: B:R.392, A:K.196

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

NAG.5: 11 residues within 4Å: Chain A: N.77, S.79, N.80, L.82, L.84, A.86, V.87, Q.89 Chain C: H.6, S.9, Y.10 8 PLIP interactions: 1 interactions with chain C, 7 interactions with chain A Hydrophobic interactions: C:Y.10 Hydrogen bonds: A:N.80, A:V.87, A:Q.89 Water bridges: A:N.77, A:N.77, A:N.77, A:S.79 NAG.15: 11 residues within 4Å: Chain B: N.77, S.79, N.80, L.82, L.84, A.86, V.87, Q.89 Chain D: H.6, S.9, Y.10 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:N.80, B:V.87, B:Q.89 Hydrophobic interactions: D:Y.10

2 x CA: CALCIUM ION(Non-covalent)

CA.6: 5 residues within 4Å: Chain A: T.56, F.58, D.60, S.62 Chain E: D.98 5 PLIP interactions: 1 interactions with chain E, 4 interactions with chain A Metal complexes: E:D.98, A:T.56, A:F.58, A:D.60, A:S.62 CA.16: 5 residues within 4Å: Chain B: T.56, F.58, D.60, S.62 Chain F: D.98 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain F Metal complexes: B:T.56, B:T.56, B:F.58, B:S.62, F:D.98

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

SCN.7: 7 residues within 4Å: Chain A: R.127, E.130, F.254, F.295 Chain E: Q.93, H.97 Ligands: HEM.14 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Water bridges: A:R.127 Hydrogen bonds: E:Q.93 SCN.8: 5 residues within 4Å: Chain A: I.178, Y.181, R.182, W.401, W.402 No protein-ligand interaction detected (PLIP) SCN.9: 3 residues within 4Å: Chain A: T.192, K.374, R.375 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.374, A:R.375 SCN.10: 8 residues within 4Å: Chain A: T.56, D.60, S.62, Y.65, G.66, S.67, R.169 Chain E: I.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.169 SCN.11: 4 residues within 4Å: Chain A: E.4, T.5, M.299, R.300 No protein-ligand interaction detected (PLIP) SCN.12: 6 residues within 4Å: Chain A: P.11, P.12, R.36, R.49 Chain E: L.45, W.49 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.49, A:R.49 SCN.13: 7 residues within 4Å: Chain A: P.39, A.40, C.41, T.47, I.48, R.49, N.50 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.50 SCN.17: 3 residues within 4Å: Chain B: E.354, Q.355 Chain F: A.61 No protein-ligand interaction detected (PLIP) SCN.18: 7 residues within 4Å: Chain B: R.127, E.130, F.254, F.295 Chain F: Q.93, H.97 Ligands: HEM.21 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:Q.93, F:H.97 Water bridges: B:R.127 SCN.19: 5 residues within 4Å: Chain B: P.331, P.333, Q.338, T.341, V.342 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.341 SCN.20: 5 residues within 4Å: Chain B: N.283, N.345, K.347, L.348, K.351 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.351 SCN.22: 10 residues within 4Å: Chain A: A.213, N.214, V.215, L.318, P.319, W.324 Chain E: R.33, W.34, L.35, A.37 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.33 SCN.23: 3 residues within 4Å: Chain E: R.72, F.73, P.74 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.72 Water bridges: E:T.75 SCN.24: 10 residues within 4Å: Chain B: A.213, N.214, V.215, L.318, P.319, W.324 Chain F: R.33, W.34, L.35, A.37 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:L.35 SCN.25: 5 residues within 4Å: Chain A: R.211 Chain B: I.48 Chain F: R.33, P.36, A.37 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.211

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.14: 28 residues within 4Å: Chain A: 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 Chain E: F.31, M.89, G.92, Q.93, D.96, D.100, F.101, T.102 Ligands: SCN.7 22 PLIP interactions: 17 interactions with chain A, 4 interactions with chain E, 1 Ligand-Water interactions, Hydrophobic interactions: A:E.130, A:M.131, A:F.220, A:R.221, A:I.227, A:F.253, A:F.295, A:L.305, A:L.305, E:Q.93, E:Q.93 Water bridges: A:R.221, A:R.221, A:R.221, A:R.221 Salt bridges: A:R.127, A:R.221, A:R.312 Metal complexes: A:H.224, H2O.2 Hydrogen bonds: E:D.100, E:T.102 HEM.21: 29 residues within 4Å: Chain B: 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 Chain F: F.31, M.89, G.92, Q.93, D.96, D.100, F.101, T.102 Ligands: SCN.18 23 PLIP interactions: 17 interactions with chain B, 5 interactions with chain F, 1 Ligand-Water interactions, Hydrophobic interactions: B:E.130, B:M.131, B:R.221, B:I.227, B:F.253, B:L.294, B:F.295, B:L.305, B:L.305, F:Q.93, F:Q.93 Water bridges: B:R.221, B:R.221, B:R.221, B:R.221 Salt bridges: B:R.127, B:R.221, B:R.312 Metal complexes: B:H.224, H2O.18 Hydrogen bonds: F:D.100, F:D.100, F:T.102

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

C
E

D
F

E
A

F
C

Myeloperoxidase heavy chain

Myeloperoxidase inhibitor SPIN

Myeloperoxidase light chain

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