SMTL ID : 9qjo.1

Structure of native leukocyte myeloperoxidase in complex with the Staphylococcal Peroxidase Inhibitor SPIN and bromide at pH 5.5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 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: 5 residues within 4Å: Chain A: N.113, A.116, W.257 Ligands: BR.17, BR.30 No protein-ligand interaction detected (PLIP)

2 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: 17 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, G.329, K.393 Chain D: W.34, L.35 Ligands: NAG-NAG-BMA-MAN-MAN-FUC.3, NAG-NAG-BMA-MAN-MAN-FUC.3, BR.7 6 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D, 1 interactions with chain B Water bridges: A:S.207 Hydrophobic interactions: D:L.35, A:V.208, A:R.392, A:K.393 Hydrogen bonds: A:R.392, B:K.393, D:W.34 NAG-NAG-BMA-MAN-MAN-FUC.3: 15 residues within 4Å: Chain A: K.196, R.326, F.327, G.329, K.393 Chain B: N.205, S.207, V.208, R.392, K.393 Chain C: W.34, L.35 Ligands: NAG-NAG-BMA-MAN-MAN-FUC.2, NAG-NAG-BMA-MAN-MAN-FUC.2, BR.40 7 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 5 interactions with chain B Water bridges: A:F.327, B:R.392, B:R.392, B:R.392 Hydrophobic interactions: C:L.35, B:V.208, B:R.392

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

NAG.4: 10 residues within 4Å: Chain A: N.77, S.79, N.80, L.84, A.86, V.87, Q.89 Chain E: H.19, S.22, Y.23 8 PLIP interactions: 1 interactions with chain E, 7 interactions with chain A Hydrophobic interactions: E:Y.23 Hydrogen bonds: A:S.79, A:S.79, A:N.80, A:V.87, A:Q.89, A:Q.89 Water bridges: A:N.77 NAG.34: 10 residues within 4Å: Chain B: N.77, S.79, N.80, L.84, A.86, V.87, Q.89 Chain F: H.19, S.22, Y.23 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:N.80, B:V.87, B:Q.89, B:Q.89 Hydrophobic interactions: F:Y.23 NAG.35: 4 residues within 4Å: Chain B: N.113, A.116, W.257 Ligands: BR.45 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.113

56 x BR: BROMIDE ION(Non-covalent)

BR.5: 5 residues within 4Å: Chain A: N.236, R.270, I.431, T.432, T.433 Ligand excluded by PLIP BR.6: 2 residues within 4Å: Chain A: P.12, R.49 Ligand excluded by PLIP BR.7: 6 residues within 4Å: Chain A: S.207, V.208, D.209, K.393 Ligands: NAG-NAG-BMA-MAN-MAN-FUC.2, NAG-NAG-BMA-MAN-MAN-FUC.2 Ligand excluded by PLIP BR.8: 4 residues within 4Å: Chain A: N.283, N.345, K.347, K.351 Ligand excluded by PLIP BR.9: 2 residues within 4Å: Chain A: K.374 Ligands: BR.29 Ligand excluded by PLIP BR.10: 4 residues within 4Å: Chain A: P.422, N.437, N.438, I.439 Ligand excluded by PLIP BR.11: 2 residues within 4Å: Chain A: Y.181, W.402 Ligand excluded by PLIP BR.12: 3 residues within 4Å: Chain A: R.96, A.97, R.143 Ligand excluded by PLIP BR.13: 4 residues within 4Å: Chain A: R.127, E.130 Chain C: H.97 Ligands: HEM.33 Ligand excluded by PLIP BR.14: 3 residues within 4Å: Chain A: R.326, N.360 Chain D: R.20 Ligand excluded by PLIP BR.15: 1 residues within 4Å: Chain A: R.300 Ligand excluded by PLIP BR.16: 3 residues within 4Å: Chain A: R.211 Chain D: R.33 Ligands: BR.64 Ligand excluded by PLIP BR.17: 5 residues within 4Å: Chain A: R.251, R.258, Q.297 Ligands: NAG-NAG.1, BR.30 Ligand excluded by PLIP BR.18: 2 residues within 4Å: Chain A: K.26, N.27 Ligand excluded by PLIP BR.19: 2 residues within 4Å: Chain A: K.436, N.437 Ligand excluded by PLIP BR.20: 1 residues within 4Å: Chain A: P.333 Ligand excluded by PLIP BR.21: 1 residues within 4Å: Chain A: P.186 Ligand excluded by PLIP BR.22: 1 residues within 4Å: Chain A: R.350 Ligand excluded by PLIP BR.23: 2 residues within 4Å: Chain A: R.163 Chain C: Y.9 Ligand excluded by PLIP BR.24: 2 residues within 4Å: Chain A: I.48 Chain D: A.30 Ligand excluded by PLIP BR.25: 2 residues within 4Å: Chain A: V.1, S.6 Ligand excluded by PLIP BR.26: 3 residues within 4Å: Chain A: M.241, P.267, R.270 Ligand excluded by PLIP BR.27: 3 residues within 4Å: Chain A: R.423, C.452, S.453 Ligand excluded by PLIP BR.28: 3 residues within 4Å: Chain A: P.19, P.20 Chain C: L.62 Ligand excluded by PLIP BR.29: 4 residues within 4Å: Chain A: T.192, A.193, K.374 Ligands: BR.9 Ligand excluded by PLIP BR.30: 4 residues within 4Å: Chain A: T.112, Q.297 Ligands: NAG-NAG.1, BR.17 Ligand excluded by PLIP BR.31: 2 residues within 4Å: Chain A: R.378 Ligands: BR.57 Ligand excluded by PLIP BR.37: 4 residues within 4Å: Chain B: R.270, I.431, T.432, T.433 Ligand excluded by PLIP BR.38: 2 residues within 4Å: Chain B: P.12, R.49 Ligand excluded by PLIP BR.39: 1 residues within 4Å: Chain B: N.345 Ligand excluded by PLIP BR.40: 6 residues within 4Å: Chain B: S.207, V.208, D.209, K.393 Ligands: NAG-NAG-BMA-MAN-MAN-FUC.3, NAG-NAG-BMA-MAN-MAN-FUC.3 Ligand excluded by PLIP BR.41: 2 residues within 4Å: Chain B: Y.181, W.402 Ligand excluded by PLIP BR.42: 4 residues within 4Å: Chain B: R.127, E.130 Chain D: H.97 Ligands: HEM.36 Ligand excluded by PLIP BR.43: 3 residues within 4Å: Chain B: R.211 Chain C: R.33 Ligands: BR.59 Ligand excluded by PLIP BR.44: 2 residues within 4Å: Chain B: I.48 Chain C: A.30 Ligand excluded by PLIP BR.45: 3 residues within 4Å: Chain B: R.258, Q.297 Ligands: NAG.35 Ligand excluded by PLIP BR.46: 3 residues within 4Å: Chain B: P.422, N.437, I.439 Ligand excluded by PLIP BR.47: 2 residues within 4Å: Chain B: P.186, P.191 Ligand excluded by PLIP BR.48: 3 residues within 4Å: Chain B: R.96, A.97, R.143 Ligand excluded by PLIP BR.49: 2 residues within 4Å: Chain B: R.378 Ligands: BR.65 Ligand excluded by PLIP BR.50: 1 residues within 4Å: Chain B: P.381 Ligand excluded by PLIP BR.51: 3 residues within 4Å: Chain B: M.410, R.413, Q.414 Ligand excluded by PLIP BR.53: 5 residues within 4Å: Chain A: N.214, V.215, W.324 Chain C: R.33, W.34 Ligand excluded by PLIP BR.54: 3 residues within 4Å: Chain C: R.72, F.73, P.74 Ligand excluded by PLIP BR.55: 3 residues within 4Å: Chain B: R.326, N.360 Chain C: R.20 Ligand excluded by PLIP BR.56: 2 residues within 4Å: Chain C: T.11, I.12 Ligand excluded by PLIP BR.57: 3 residues within 4Å: Chain A: K.376 Chain C: R.84 Ligands: BR.31 Ligand excluded by PLIP BR.58: 5 residues within 4Å: Chain A: P.229, D.288, E.289, R.293 Chain C: T.75 Ligand excluded by PLIP BR.59: 4 residues within 4Å: Chain A: I.48 Chain C: P.36, A.37 Ligands: BR.43 Ligand excluded by PLIP BR.60: 5 residues within 4Å: Chain B: N.214, V.215, W.324 Chain D: R.33, W.34 Ligand excluded by PLIP BR.61: 5 residues within 4Å: Chain B: P.229, D.288, E.289, R.293 Chain D: T.75 Ligand excluded by PLIP BR.62: 2 residues within 4Å: Chain D: G.52, P.59 Ligand excluded by PLIP BR.63: 3 residues within 4Å: Chain D: M.15, T.23, R.29 Ligand excluded by PLIP BR.64: 4 residues within 4Å: Chain B: I.48 Chain D: P.36, A.37 Ligands: BR.16 Ligand excluded by PLIP BR.65: 3 residues within 4Å: Chain B: K.376 Chain D: R.84 Ligands: BR.49 Ligand excluded by PLIP BR.66: 5 residues within 4Å: Chain B: Q.89, P.100, F.101 Chain F: E.18, H.19 Ligand excluded by PLIP

2 x CA: CALCIUM ION(Non-covalent)

CA.32: 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:T.56, A:F.58, A:S.62, C:D.98, C:D.98 CA.52: 5 residues within 4Å: Chain B: T.56, F.58, D.60, S.62 Chain D: D.98 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain B Metal complexes: D:D.98, D:D.98, B:T.56, B:F.58, B:S.62

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.33: 24 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 Chain E: Q.5, N.6 Ligands: BR.13 27 PLIP interactions: 18 interactions with chain A, 3 interactions with chain E, 6 interactions with chain C, Hydrophobic interactions: A:E.130, A:M.131, A:R.221, A:I.227, A:F.253, A:F.295, A:L.305, A:L.305, C:Q.93, C:Q.93 Water bridges: A:R.127, A:T.217, A:R.221, A:R.221, A:R.221, A:R.221, E:N.6 Salt bridges: A:R.127, A:R.221, A:R.312 Metal complexes: A:H.224 Hydrogen bonds: E:Q.5, E:N.6, C:D.100, C:D.100, C:T.102, C:T.102 HEM.36: 25 residues within 4Å: Chain B: 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, L.308, R.312 Chain D: M.89, G.92, Q.93, D.96, D.100, F.101, T.102 Chain F: Q.5, N.6 Ligands: BR.42 21 PLIP interactions: 14 interactions with chain B, 3 interactions with chain F, 3 interactions with chain D, 1 Ligand-Water interactions, Hydrophobic interactions: B:E.130, B:M.131, B:R.221, 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, B:R.221, F:Q.5 Salt bridges: B:R.127, B:R.221, B:R.312 Metal complexes: B:H.224, H2O.12 Hydrogen bonds: F:Q.5, F:N.6, D: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 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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