SMTL ID : 9sds.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

hetero-1-1-1-mer

Ligands

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.1: 7 residues within 4Å: Chain B: R.202, N.205, S.207, V.208, R.392, K.393, D.396 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.208 Hydrogen bonds: B:R.392, B:K.393

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.2: 9 residues within 4Å: Chain B: N.77, S.79, N.80, L.84, A.86, V.87, Q.89, Q.92 Chain C: H.6 No protein-ligand interaction detected (PLIP)

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.3: 22 residues within 4Å: Chain A: M.89, G.92, Q.93, D.96, D.100, F.101, T.102 Chain B: R.127, E.130, M.131, T.217, F.220, R.221, G.223, H.224, I.227, F.253, L.294, F.295, L.305, L.308, R.312 21 PLIP interactions: 17 interactions with chain B, 4 interactions with chain A, Hydrophobic interactions: B:E.130, B:M.131, B:F.220, B:F.220, B:R.221, B:I.227, B:F.253, B:L.294, B:F.295, B:L.305, B:L.305, A:Q.93, A:Q.93 Water bridges: B:R.127, B:R.127, A:T.102 Salt bridges: B:R.127, B:R.221, B:R.312 Metal complexes: B:H.224 Hydrogen bonds: A:T.102

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

IOD.4: 5 residues within 4Å: Chain A: R.33, W.34 Chain B: N.214, V.215, W.324 Ligand excluded by PLIP

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

NAG.5: 5 residues within 4Å: Chain B: N.113, S.115, N.244, W.257, L.261 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

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

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 2 residues within 4Å: Chain B: R.127, E.130 Ligand excluded by PLIP

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: A
Myeloperoxidase: B
Myeloperoxidase inhibitor SPIN: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

C
F

Myeloperoxidase light chain

Myeloperoxidase

Myeloperoxidase inhibitor SPIN

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