SMTL ID : 4dl1.4 (11 other biounits)

Crystal Structure of human Myeloperoxidase with covalent thioxanthine analog

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-2-2-mer

Ligands

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(Non-functional Binders)(Covalent)

NAG-NAG-BMA-MAN-MAN-FUC.1: 14 residues within 4Å: Chain B: N.205, S.207, V.208, R.392 Chain C: W.32, L.33 Chain D: K.196, Y.197, R.326, F.327, G.329, K.393 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 D, 1 interactions with chain C Hydrophobic interactions: B:V.208, C:L.33 Hydrogen bonds: D:K.393 Water bridges: B:S.207 NAG-NAG-BMA-MAN-MAN-FUC.2: 14 residues within 4Å: Chain A: W.32, L.33 Chain B: K.196, Y.197, R.326, F.327, G.329, K.393 Chain D: N.205, S.207, V.208, R.392 Ligands: NAG-NAG-BMA-MAN-MAN-FUC.1, NAG-NAG-BMA-MAN-MAN-FUC.1 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: D:V.208, A:L.33 Hydrogen bonds: D:R.392, B:K.393 Water bridges: D:S.207

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.3: 8 residues within 4Å: Chain D: N.77, N.80, L.84, A.86, V.87, Q.89, R.90, Q.92 2 PLIP interactions: 2 interactions with chain D Water bridges: D:Q.92, D:Q.92, D:Q.89, D:Q.92

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

CL.4: 5 residues within 4Å: Chain A: R.31, W.32 Chain B: N.214, V.215, W.324 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain C: R.31, W.32 Chain D: N.214, V.215, W.324 Ligand excluded by PLIP

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.5: 22 residues within 4Å: Chain A: M.87, G.90, Q.91, D.94, D.98, F.99, T.100 Chain B: 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 Ligands: 0KY.9 22 PLIP interactions: 16 interactions with chain B, 5 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: B:E.130, B:M.131, B:F.220, B:R.221, B:I.227, B:F.253, B:F.295, B:L.305, B:L.305, A:Q.91, A:Q.91 Water bridges: B:R.221, B:R.221, B:R.221 Salt bridges: B:R.127, B:R.221, B:R.312 Metal complexes: B:H.224, H2O.1 Hydrogen bonds: A:D.98, A:T.100, A:T.100 HEM.11: 25 residues within 4Å: Chain C: M.87, G.90, Q.91, D.94, D.98, F.99, T.100 Chain D: R.127, E.130, M.131, Y.184, T.217, F.220, R.221, Y.222, G.223, H.224, I.227, F.253, L.294, F.295, L.305, L.308, R.312 Ligands: 0KY.14 22 PLIP interactions: 17 interactions with chain D, 4 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: D:E.130, D:M.131, D:F.220, D:R.221, D:Y.222, D:I.227, D:F.253, D:L.294, D:F.295, D:L.305, D:L.305, C:Q.91, C:Q.91 Water bridges: D:R.221, D:R.221 Salt bridges: D:R.127, D:R.221, D:R.312 Metal complexes: D:H.224, H2O.12 Hydrogen bonds: C:D.98, C:T.100

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

NAG.6: 6 residues within 4Å: Chain B: N.77, N.80, L.84, A.86, V.87, Q.89 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.80, B:V.87, B:Q.89, B:Q.89 Water bridges: B:N.77, B:S.79, B:S.79 NAG.7: 3 residues within 4Å: Chain B: N.113, A.116, W.257 No protein-ligand interaction detected (PLIP) NAG.13: 5 residues within 4Å: Chain D: N.113, S.115, A.116, W.257, L.261 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.113

2 x CA: CALCIUM ION(Non-covalent)

CA.8: 5 residues within 4Å: Chain A: D.96 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.96 CA.12: 5 residues within 4Å: Chain C: D.96 Chain D: T.56, F.58, D.60, S.62 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Metal complexes: D:T.56, D:F.58, D:S.62, C:D.96, C:D.96

2 x 0KY: 3-[(2R)-2-ethoxypropyl]-2-thioxo-1,2,3,9-tetrahydro-6H-purin-6-one(Non-covalent)

0KY.9: 5 residues within 4Å: Chain B: R.127, E.130, F.254, F.295 Ligands: HEM.5 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.254, B:F.295 0KY.14: 5 residues within 4Å: Chain D: E.4, R.127, E.130, F.295 Ligands: HEM.11 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C pi-Stacking: D:F.295 Water bridges: C:Q.91

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Geoghegan, K.F. et al., Deconstruction of activity-dependent covalent modification of heme in human neutrophil myeloperoxidase by multistage mass spectrometry (MS(4)). Biochemistry (2012)

Release Date

2012-03-21

Peptides

Myeloperoxidase light chain: AC
Myeloperoxidase heavy chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
M

C
N

B
O

D
P

Myeloperoxidase light chain

Myeloperoxidase heavy chain

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