SMTL ID : 9qj3.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.63 Å

Oligo State

hetero-2-2-2-mer

Ligands

4 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: 9 residues within 4Å: Chain A: N.77, S.79, N.80, A.86, V.87, Q.89 Chain E: H.6, S.9, Y.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.89 NAG-NAG.2: 5 residues within 4Å: Chain A: N.113, S.115, A.116, W.257 Ligands: IOD.22 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 8 residues within 4Å: Chain B: N.77, S.79, N.80, A.86, V.87, Q.89 Chain F: H.6, S.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.89 NAG-NAG.5: 7 residues within 4Å: Chain B: N.113, S.115, A.116, W.257, L.261 Ligands: IOD.62, IOD.75 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- NAG- MAN- MAN- FUC: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose-(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-NAG-MAN-MAN-FUC.3: 15 residues within 4Å: Chain A: N.205, S.207, V.208, R.392, K.393 Chain B: K.196, Y.197, R.326, F.327, G.329, K.393 Chain D: W.34, L.35 Ligands: NAG-NAG-BMA-MAN-MAN-FUC.6, NAG-NAG-BMA-MAN-MAN-FUC.6 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:K.393 Hydrogen bonds: A:R.392, A:K.393, B:K.393, B:K.393

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.6: 17 residues within 4Å: Chain A: K.196, Y.197, R.326, F.327, G.329, K.393 Chain B: R.202, N.205, S.207, V.208, R.392, K.393 Chain C: W.34, L.35 Ligands: NAG-NAG-NAG-MAN-MAN-FUC.3, NAG-NAG-NAG-MAN-MAN-FUC.3, IOD.61 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: C:L.35, B:V.208 Water bridges: B:R.392 Hydrogen bonds: A:K.393, C:W.34

89 x IOD: IODIDE ION(Non-functional Binders)

IOD.7: 3 residues within 4Å: Chain A: R.270, T.432, T.433 Ligand excluded by PLIP IOD.8: 1 residues within 4Å: Chain A: W.402 Ligand excluded by PLIP IOD.9: 1 residues within 4Å: Chain A: R.300 Ligand excluded by PLIP IOD.10: 4 residues within 4Å: Chain A: Q.89, F.101 Chain E: E.5, H.6 Ligand excluded by PLIP IOD.11: 3 residues within 4Å: Chain A: R.96, A.97, R.143 Ligand excluded by PLIP IOD.12: 2 residues within 4Å: Chain A: T.192, K.374 Ligand excluded by PLIP IOD.13: 2 residues within 4Å: Chain A: P.12, R.49 Ligand excluded by PLIP IOD.14: 5 residues within 4Å: Chain A: R.127, E.130 Chain C: H.97 Ligands: IOD.46, HEM.84 Ligand excluded by PLIP IOD.15: 2 residues within 4Å: Chain A: P.331, P.333 Ligand excluded by PLIP IOD.16: 3 residues within 4Å: Chain A: R.326, N.360 Chain D: R.20 Ligand excluded by PLIP IOD.17: 2 residues within 4Å: Chain A: R.163 Chain C: Y.9 Ligand excluded by PLIP IOD.18: 4 residues within 4Å: Chain A: N.283, N.345, K.347, K.351 Ligand excluded by PLIP IOD.19: 1 residues within 4Å: Chain A: P.191 Ligand excluded by PLIP IOD.20: 3 residues within 4Å: Chain A: D.235, N.236, M.241 Ligand excluded by PLIP IOD.21: 1 residues within 4Å: Chain A: K.26 Ligand excluded by PLIP IOD.22: 3 residues within 4Å: Chain A: T.112, Q.297 Ligands: NAG-NAG.2 Ligand excluded by PLIP IOD.23: 2 residues within 4Å: Chain A: A.40 Ligands: IOD.47 Ligand excluded by PLIP IOD.24: 2 residues within 4Å: Chain A: K.347, R.350 Ligand excluded by PLIP IOD.25: 2 residues within 4Å: Chain A: I.419, R.423 Ligand excluded by PLIP IOD.26: 3 residues within 4Å: Chain A: K.374, R.375 Ligands: IOD.43 Ligand excluded by PLIP IOD.27: 1 residues within 4Å: Chain A: P.248 Ligand excluded by PLIP IOD.28: 2 residues within 4Å: Chain A: D.209, K.393 Ligand excluded by PLIP IOD.29: 3 residues within 4Å: Chain A: K.351, E.354, Q.355 Ligand excluded by PLIP IOD.30: 3 residues within 4Å: Chain A: F.232, P.240, R.246 Ligand excluded by PLIP IOD.31: 1 residues within 4Å: Chain A: R.281 Ligand excluded by PLIP IOD.32: 1 residues within 4Å: Chain A: R.325 Ligand excluded by PLIP IOD.33: 2 residues within 4Å: Chain A: M.441 Chain C: R.84 Ligand excluded by PLIP IOD.34: 2 residues within 4Å: Chain A: R.413, Q.414 Ligand excluded by PLIP IOD.35: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.36: 1 residues within 4Å: Chain A: R.447 Ligand excluded by PLIP IOD.37: 1 residues within 4Å: Chain A: F.408 Ligand excluded by PLIP IOD.38: 2 residues within 4Å: Chain A: R.423, S.453 Ligand excluded by PLIP IOD.39: 2 residues within 4Å: Chain A: C.452, S.453 Ligand excluded by PLIP IOD.40: 1 residues within 4Å: Chain A: R.350 Ligand excluded by PLIP IOD.41: 2 residues within 4Å: Chain A: Q.81, L.82 Ligand excluded by PLIP IOD.42: 3 residues within 4Å: Chain A: R.281, Q.282, N.283 Ligand excluded by PLIP IOD.43: 3 residues within 4Å: Chain A: T.192, K.374 Ligands: IOD.26 Ligand excluded by PLIP IOD.44: 1 residues within 4Å: Chain A: Q.414 Ligand excluded by PLIP IOD.45: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.46: 2 residues within 4Å: Chain A: R.127 Ligands: IOD.14 Ligand excluded by PLIP IOD.47: 4 residues within 4Å: Chain A: T.47 Chain B: T.47 Ligands: IOD.23, IOD.79 Ligand excluded by PLIP IOD.50: 5 residues within 4Å: Chain B: N.214, V.215, W.324 Chain D: R.33, W.34 Ligand excluded by PLIP IOD.51: 5 residues within 4Å: Chain B: N.236, R.270, I.431, T.432, T.433 Ligand excluded by PLIP IOD.52: 1 residues within 4Å: Chain B: W.402 Ligand excluded by PLIP IOD.53: 2 residues within 4Å: Chain B: N.345, K.351 Ligand excluded by PLIP IOD.54: 4 residues within 4Å: Chain B: Q.89, F.101 Chain F: E.5, H.6 Ligand excluded by PLIP IOD.55: 1 residues within 4Å: Chain B: R.325 Ligand excluded by PLIP IOD.56: 4 residues within 4Å: Chain B: R.127, E.130 Ligands: HEM.49, IOD.78 Ligand excluded by PLIP IOD.57: 2 residues within 4Å: Chain B: P.12, R.49 Ligand excluded by PLIP IOD.58: 1 residues within 4Å: Chain B: P.331 Ligand excluded by PLIP IOD.59: 2 residues within 4Å: Chain B: A.97, R.143 Ligand excluded by PLIP IOD.60: 2 residues within 4Å: Chain B: P.186, P.191 Ligand excluded by PLIP IOD.61: 4 residues within 4Å: Chain B: V.208, D.209, K.393 Ligands: NAG-NAG-BMA-MAN-MAN-FUC.6 Ligand excluded by PLIP IOD.62: 2 residues within 4Å: Chain B: Q.297 Ligands: NAG-NAG.5 Ligand excluded by PLIP IOD.63: 2 residues within 4Å: Chain B: R.378 Ligands: IOD.80 Ligand excluded by PLIP IOD.64: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.65: 1 residues within 4Å: Chain B: R.163 Ligand excluded by PLIP IOD.66: 3 residues within 4Å: Chain B: G.329, L.330, P.331 Ligand excluded by PLIP IOD.67: 1 residues within 4Å: Chain B: Q.228 Ligand excluded by PLIP IOD.68: 2 residues within 4Å: Chain B: K.374 Ligands: IOD.81 Ligand excluded by PLIP IOD.69: 1 residues within 4Å: Chain B: N.27 Ligand excluded by PLIP IOD.70: 2 residues within 4Å: Chain B: R.350, E.354 Ligand excluded by PLIP IOD.71: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.72: 3 residues within 4Å: Chain B: R.423, C.452, S.453 Ligand excluded by PLIP IOD.73: 1 residues within 4Å: Chain B: R.246 Ligand excluded by PLIP IOD.74: 2 residues within 4Å: Chain B: I.419, R.423 Ligand excluded by PLIP IOD.75: 2 residues within 4Å: Ligands: NAG-NAG.5, NAG-NAG.5 Ligand excluded by PLIP IOD.76: 1 residues within 4Å: Chain B: R.251 Ligand excluded by PLIP IOD.77: 1 residues within 4Å: Chain B: R.375 Ligand excluded by PLIP IOD.78: 1 residues within 4Å: Ligands: IOD.56 Ligand excluded by PLIP IOD.79: 1 residues within 4Å: Ligands: IOD.47 Ligand excluded by PLIP IOD.80: 2 residues within 4Å: Chain D: R.84 Ligands: IOD.63 Ligand excluded by PLIP IOD.81: 4 residues within 4Å: Chain B: T.192, K.196, K.374 Ligands: IOD.68 Ligand excluded by PLIP IOD.82: 4 residues within 4Å: Chain B: D.235, N.236, M.241, R.270 Ligand excluded by PLIP IOD.85: 5 residues within 4Å: Chain A: N.214, V.215, W.324 Chain C: R.33, W.34 Ligand excluded by PLIP IOD.86: 1 residues within 4Å: Chain C: R.72 Ligand excluded by PLIP IOD.87: 3 residues within 4Å: Chain A: I.48 Chain B: R.211 Chain C: A.37 Ligand excluded by PLIP IOD.88: 3 residues within 4Å: Chain B: R.326, N.360 Chain C: R.20 Ligand excluded by PLIP IOD.89: 2 residues within 4Å: Chain C: G.52, P.59 Ligand excluded by PLIP IOD.90: 2 residues within 4Å: Chain C: C.3 Chain D: E.40 Ligand excluded by PLIP IOD.91: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.92: 1 residues within 4Å: Chain C: P.59 Ligand excluded by PLIP IOD.93: 1 residues within 4Å: Chain C: Q.6 Ligand excluded by PLIP IOD.94: 3 residues within 4Å: Chain A: R.211 Chain B: I.48 Chain D: A.37 Ligand excluded by PLIP IOD.95: 2 residues within 4Å: Chain D: G.52, P.59 Ligand excluded by PLIP IOD.96: 2 residues within 4Å: Chain B: P.276 Chain D: Q.82 Ligand excluded by PLIP IOD.97: 1 residues within 4Å: Chain D: C.3 Ligand excluded by PLIP IOD.98: 1 residues within 4Å: Chain A: N.74 Ligand excluded by PLIP IOD.99: 1 residues within 4Å: Chain F: K.40 Ligand excluded by PLIP

2 x CA: CALCIUM ION(Non-covalent)

CA.48: 5 residues within 4Å: Chain A: T.56, F.58, D.60, S.62 Chain C: D.98 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Metal complexes: A:F.58, A:D.60, A:S.62, C:D.98, C:D.98 CA.83: 5 residues within 4Å: Chain B: T.56, F.58, D.60, S.62 Chain D: D.98 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain B Metal complexes: D:D.98, B:T.56, B:F.58, B:D.60, B:S.62

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.49: 23 residues within 4Å: Chain B: R.127, E.130, M.131, T.217, F.220, R.221, Y.222, G.223, H.224, I.227, F.253, F.295, L.305, L.308, R.312 Chain D: M.89, G.92, Q.93, D.96, D.100, F.101, T.102 Ligands: IOD.56 18 PLIP interactions: 15 interactions with chain B, 3 interactions with chain D, Hydrophobic interactions: B:E.130, B:M.131, B:F.220, B:R.221, B:Y.222, B:I.227, B:F.253, B:F.295, B:L.305, B:L.305, D:Q.93, D:Q.93 Water bridges: B:R.221 Salt bridges: B:R.127, B:R.221, B:R.312 Metal complexes: B:H.224 Hydrogen bonds: D:T.102 HEM.84: 22 residues within 4Å: Chain A: 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 Chain C: M.89, G.92, Q.93, D.96, D.100, F.101, T.102 Ligands: IOD.14 24 PLIP interactions: 6 interactions with chain C, 18 interactions with chain A, Hydrophobic interactions: C:Q.93, C:Q.93, C:D.96, 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 Hydrogen bonds: C:D.100, C:T.102, C:T.102 Water bridges: A:R.127, A:R.127, A:T.217, A:R.221, A:R.221 Salt bridges: A:R.127, A:R.221, A:R.312 Metal complexes: A:H.224

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 light chain: CD
Myeloperoxidase inhibitor SPIN: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

C
A

D
C

E
E

F
F

Myeloperoxidase heavy chain

Myeloperoxidase light chain

Myeloperoxidase inhibitor SPIN

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