SMTL ID : 3zs0.1

Human Myeloperoxidase inactivated by TX2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-2-2-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: 13 residues within 4Å: Chain B: W.34, L.35 Chain C: N.205, S.207, V.208 Chain D: K.196, Y.197, R.326, F.327, G.329, K.393 Ligands: NAG-NAG-BMA-MAN-FUC.2, NAG-NAG-BMA-MAN-FUC.2 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: C:V.208, B:L.35 Hydrogen bonds: B:W.34, D:K.393 Water bridges: C:S.207

1 x NAG- NAG- BMA- MAN- FUC: 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-FUC.2: 13 residues within 4Å: Chain A: W.34, L.35 Chain C: 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 C, 1 interactions with chain A Hydrophobic interactions: D:V.208, A:L.35 Hydrogen bonds: C:K.393 Water bridges: D:S.207

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 3 residues within 4Å: Chain B: T.75 Chain D: D.288, R.293 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B Water bridges: D:D.288, D:R.293 Salt bridges: D:R.293 Hydrogen bonds: B:T.75, B:T.75 SO4.10: 3 residues within 4Å: Chain A: T.75 Chain C: D.288, R.293 11 PLIP interactions: 7 interactions with chain C, 4 interactions with chain A Water bridges: C:D.288, C:R.293, C:R.293, C:R.293, C:R.293, C:R.293, A:T.75, A:T.75 Salt bridges: C:R.293 Hydrogen bonds: A:T.75, A:T.75 SO4.11: 1 residues within 4Å: Chain C: R.117 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.117

2 x ZS0: 3-(4-FLUOROBENZYL)-2-THIOXO-1,2,3,7-TETRAHYDRO-6H-PURIN-6-ONE(Non-covalent)

ZS0.4: 7 residues within 4Å: Chain A: E.104 Chain C: P.33, R.127, F.295, M.299, L.303 Ligands: HEM.5 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.303 ZS0.15: 8 residues within 4Å: Chain B: E.104 Chain D: P.33, R.127, E.130, F.295, M.299, L.303 Ligands: HEM.16 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.303

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.5: 24 residues within 4Å: Chain A: M.89, G.92, Q.93, D.96, D.100, F.101, T.102 Chain C: R.127, E.130, M.131, Y.184, T.217, F.220, R.221, Y.222, G.223, H.224, I.227, F.253, F.295, L.305, L.308, R.312 Ligands: ZS0.4 23 PLIP interactions: 17 interactions with chain C, 5 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: C:E.130, C:M.131, C:F.220, C:R.221, C:Y.222, C:I.227, C:F.253, C:F.295, C:L.305, C:L.305, A:Q.93, A:Q.93, A:D.96 Water bridges: C:R.221, C:R.221, C:R.221 Salt bridges: C:R.127, C:R.221, C:R.312 Metal complexes: C:H.224, H2O.4 Hydrogen bonds: A:D.100, A:T.102 HEM.16: 24 residues within 4Å: Chain B: M.89, G.92, Q.93, D.96, D.100, F.101, T.102 Chain D: R.127, E.130, M.131, Y.184, T.217, F.220, R.221, G.223, H.224, I.227, F.253, L.294, F.295, L.305, L.308, R.312 Ligands: ZS0.15 24 PLIP interactions: 17 interactions with chain D, 6 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: D:E.130, D:M.131, D:F.220, D:R.221, D:I.227, D:F.253, D:L.294, D:L.294, D:F.295, D:L.305, D:L.305, B:Q.93, B:Q.93 Water bridges: D:T.217, D:R.221 Salt bridges: D:R.127, D:R.221, D:R.312 Metal complexes: D:H.224, H2O.7 Hydrogen bonds: B:D.100, B:D.100, B:T.102, B:T.102

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

NAG.6: 6 residues within 4Å: Chain C: N.77, N.80, L.84, A.86, V.87, Q.89 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.80, C:V.87, C:Q.89, C:Q.89 Water bridges: C:N.77 NAG.7: 4 residues within 4Å: Chain C: N.113, A.116, W.257, L.261 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.113 NAG.17: 5 residues within 4Å: Chain D: N.77, N.80, A.86, V.87, Q.89 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:N.80, D:V.87, D:Q.89, D:Q.89 Water bridges: D:N.77 NAG.18: 4 residues within 4Å: Chain D: N.113, A.116, W.257, L.261 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.113 Water bridges: D:S.115

2 x CA: CALCIUM ION(Non-covalent)

CA.8: 5 residues within 4Å: Chain A: D.98 Chain C: T.56, F.58, D.60, S.62 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Metal complexes: C:T.56, C:F.58, C:D.60, C:S.62, A:D.98 CA.22: 5 residues within 4Å: Chain B: D.98 Chain D: T.56, F.58, D.60, S.62 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B Metal complexes: D:T.56, D:F.58, D:S.62, B:D.98, B:D.98

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

CL.9: 5 residues within 4Å: Chain A: R.33, W.34 Chain C: N.214, V.215, W.324 Ligand excluded by PLIP CL.23: 5 residues within 4Å: Chain B: R.33, W.34 Chain D: N.214, V.215, W.324 Ligand excluded by PLIP

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.12: 1 residues within 4Å: Chain C: R.413 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.413 ACT.13: 3 residues within 4Å: Chain C: P.11, P.12, R.49 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:P.11 Water bridges: C:R.36, C:R.49, C:R.49 Salt bridges: C:R.49 ACT.14: 3 residues within 4Å: Chain C: P.191, R.195, R.375 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:P.191 Salt bridges: C:R.195, C:R.375 ACT.19: 4 residues within 4Å: Chain D: P.11, P.12, P.39, R.49 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:P.39 Water bridges: D:R.49, D:R.49 Salt bridges: D:R.49 ACT.20: 2 residues within 4Å: Chain D: M.410, R.413 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.413 ACT.21: 3 residues within 4Å: Chain D: P.191, R.195, R.375 3 PLIP interactions: 3 interactions with chain D Salt bridges: D:R.195, D:R.375, D:K.376

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tiden, A.K. et al., 2-Thioxanthines are Mechanism-Based Inactivators of Myeloperoxidase that Block Oxidative Stress During Inflammation. J.Biol.Chem. (2011)

Release Date

2011-08-31

Peptides

MYELOPEROXIDASE LIGHT CHAIN: AB
MYELOPEROXIDASE HEAVY CHAIN: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

MYELOPEROXIDASE LIGHT CHAIN

MYELOPEROXIDASE HEAVY CHAIN

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