SMTL ID : 7z53.2 (3 other biounits)

Structure of native leukocyte myeloperoxidase in complex with a truncated version (SPIN truncated) of the Staphyloccal Peroxidase Inhibitor SPIN from Staphylococcus aureus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.28 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: 11 residues within 4Å: Chain B: N.77, S.79, N.80, L.82, L.84, A.86, V.87, Q.89 Chain E: H.6, S.9, Y.10 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain D: N.113, S.115, A.116, P.243, W.257, L.261 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: 19 residues within 4Å: Chain B: N.205, S.207, V.208, R.392, K.393, D.396 Chain C: W.33, L.34 Chain D: K.196, Y.197, R.326, F.327, C.328, G.329, C.385, T.389, K.393 Ligands: NAG-NAG-BMA-MAN-MAN-FUC.5, NAG-NAG-BMA-MAN-MAN-FUC.5 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: C:L.34, B:V.208 Hydrogen bonds: D:F.327, D:K.393 Water bridges: B:K.393 NAG-NAG-BMA-MAN-MAN-FUC.5: 20 residues within 4Å: Chain A: W.33, L.34 Chain B: K.196, Y.197, R.326, F.327, C.328, G.329, C.385, T.389, K.393 Chain D: R.202, N.205, S.207, V.208, R.392, K.393, D.396 Ligands: NAG-NAG-BMA-MAN-MAN-FUC.2, NAG-NAG-BMA-MAN-MAN-FUC.2 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: B:R.326, B:F.327, B:K.393 Water bridges: B:F.327, B:C.328 Hydrophobic interactions: A:L.34, D:V.208

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 12 residues within 4Å: Chain D: N.77, S.79, N.80, L.82, L.84, A.86, V.87, Q.89, Q.92 Chain F: H.6, S.9, Y.10 No protein-ligand interaction detected (PLIP)

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

CL.6: 9 residues within 4Å: Chain A: V.31, R.32, W.33, L.34 Chain B: A.213, N.214, V.215, L.318, W.324 Ligand excluded by PLIP CL.10: 8 residues within 4Å: Chain C: R.32, W.33, L.34 Chain D: A.213, N.214, V.215, L.318, W.324 Ligand excluded by PLIP

2 x HEC: HEME C(Covalent)

HEC.7: 29 residues within 4Å: Chain A: F.30, M.88, G.91, Q.92, D.95, D.99, F.100, T.101 Chain B: F.34, R.127, E.130, M.131, Y.184, F.216, 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 20 PLIP interactions: 6 interactions with chain A, 14 interactions with chain B, Hydrophobic interactions: A:Q.92, A:Q.92, 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 Hydrogen bonds: A:D.99, A:D.99, A:T.101, A:T.101 Water bridges: B:R.221 Salt bridges: B:R.127, B:R.221, B:R.312 Metal complexes: B:H.224 HEC.11: 29 residues within 4Å: Chain C: F.30, M.88, Q.89, G.91, Q.92, D.95, D.99, F.100, T.101 Chain D: 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, I.290, L.294, F.295, L.305, L.308, N.309, R.312 19 PLIP interactions: 12 interactions with chain D, 7 interactions with chain C, Hydrophobic interactions: D:M.131, D:R.221, D:I.227, D:F.253, D:L.294, D:F.295, D:L.305, D:L.305, C:Q.92, C:Q.92, C:D.95 Salt bridges: D:R.127, D:R.221, D:R.312 Metal complexes: D:H.224 Hydrogen bonds: C:D.99, C:D.99, C:T.101, C:T.101

2 x CA: CALCIUM ION(Non-covalent)

CA.8: 6 residues within 4Å: Chain A: D.97, L.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 CA.12: 6 residues within 4Å: Chain C: D.97, L.98 Chain D: T.56, F.58, D.60, S.62 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Metal complexes: C:D.97, C:D.97, D:T.56, D:F.58, D:S.62

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

NAG.9: 5 residues within 4Å: Chain B: N.113, S.115, A.116, W.257, L.261 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.113

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: AC
Myeloperoxidase heavy chain: BD
Myeloperoxidase inhibitor SPIN: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

C
I

B
H

D
J

E
K

F
L

Myeloperoxidase light chain

Myeloperoxidase heavy chain

Myeloperoxidase inhibitor SPIN

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