SMTL ID : 7qzr.1 (1 other biounit)

Structure of native leukocyte myeloperoxidase in complex with the Staphyloccal Peroxidase Inhibitor SPIN from Staphylococcus aureus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

hetero-1-1-1-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: 12 residues within 4Å: Chain B: N.77, S.79, N.80, L.82, L.84, A.86, V.87, Q.89, Q.92 Chain C: H.48, S.51, Y.52 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.89 NAG-NAG.2: 6 residues within 4Å: Chain B: N.113, S.115, A.116, P.243, W.257, 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.3: 6 residues within 4Å: Chain B: N.205, S.207, V.208, R.392, K.393, D.396 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.208

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 5 residues within 4Å: Chain A: R.33, W.34, L.35, P.36, A.37 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.33 Water bridges: A:A.37 EDO.8: 8 residues within 4Å: Chain A: V.32, W.34 Chain B: D.209, P.210, R.211, A.213, Q.390, K.393 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:W.34, B:D.209, B:K.393 EDO.9: 6 residues within 4Å: Chain B: L.279, N.280, R.281, Q.282, P.372, L.373 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.280, B:L.373 EDO.12: 3 residues within 4Å: Chain A: V.32 Chain B: D.209, R.211 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.211, B:R.211

1 x HEC: HEME C(Covalent)

HEC.5: 34 residues within 4Å: Chain A: F.31, M.89, Q.90, G.92, Q.93, D.96, D.100, F.101, T.102 Chain B: F.34, R.127, E.130, M.131, L.134, Y.184, F.216, T.217, F.220, R.221, Y.222, G.223, H.224, L.226, I.227, L.249, F.253, L.294, F.295, L.305, L.308, N.309, R.312 Chain C: Q.34, N.35 24 PLIP interactions: 17 interactions with chain B, 4 interactions with chain A, 3 interactions with chain C, Hydrophobic interactions: B:E.130, B:F.220, B:F.220, B:R.221, B:I.227, B:F.253, B:L.294, B:L.294, B:F.295, B:L.305, A:Q.93, A:Q.93 Water bridges: B:R.127, B:R.221, B:R.221 Salt bridges: B:R.127, B:R.221, B:R.312 Metal complexes: B:H.224 Hydrogen bonds: A:D.100, A:T.102, C:Q.34, C:N.35, C:N.35

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

CL.6: 8 residues within 4Å: Chain A: R.33, W.34, L.35 Chain B: A.213, N.214, V.215, L.318, W.324 Ligand excluded by PLIP

1 x CA: CALCIUM ION(Non-covalent)

CA.7: 6 residues within 4Å: Chain A: D.98, L.99 Chain B: T.56, F.58, D.60, S.62 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Metal complexes: B:T.56, B:F.58, B:D.60, B:S.62, A:D.98

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.10: 7 residues within 4Å: Chain A: R.19 Chain B: R.399, F.400, N.404, E.405, G.406, V.407 3 PLIP interactions: 3 interactions with chain B Water bridges: B:N.404, B:N.404 Salt bridges: B:R.399

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.11: 4 residues within 4Å: Chain B: S.444, Y.445, P.446, R.447 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.444, B:R.447 Water bridges: B:R.447

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leitgeb, U. et al., The staphylococcal inhibitory protein SPIN binds to human myeloperoxidase with picomolar affinity but only dampens halide oxidation. J.Biol.Chem. (2022)

Release Date

2022-10-26

Peptides

Myeloperoxidase light chain: A
Myeloperoxidase heavy chain: B
Exported protein: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

Myeloperoxidase light chain

Myeloperoxidase heavy chain

Exported protein

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