SMTL ID : 4c1m.1 (1 other biounit)

Myeloperoxidase in complex with the revesible inhibitor HX1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- FUC: alpha-D-mannopyranose-(1-4)-[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(Covalent)

NAG-NAG-BMA-MAN-MAN-FUC.1: 4 residues within 4Å: Chain B: N.205, S.207, V.208, R.392 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.392

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.2: 25 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, 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: NIH.3 21 PLIP interactions: 5 interactions with chain A, 16 interactions with chain B, Hydrophobic interactions: A:Q.93, B:M.131, B:R.221, B:Y.222, B:I.227, B:F.253, B:L.294, B:L.294, B:F.295, B:L.305, B:L.305 Hydrogen bonds: A:D.100, A:D.100, A:T.102 Water bridges: A:T.102, B:R.221, B:R.312 Salt bridges: B:R.127, B:R.221, B:R.312 Metal complexes: B:H.224

1 x NIH: 2-{[3,5-BIS(TRIFLUOROMETHYL)BENZYL]AMINO}-N-HYDROXY-6-OXO-1,6-DIHYDROPYRIMIDINE-5-CARBOXAMIDE(Non-covalent)

NIH.3: 12 residues within 4Å: Chain A: Q.93, H.97, F.101 Chain B: P.108, T.126, R.127, E.130, F.254, F.295, V.298, M.299 Ligands: HEM.2 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.93, B:R.127 Water bridges: A:E.104, A:E.104 Hydrophobic interactions: B:F.254

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

SO4.4: 0 residues within 4Å: (No contacts) 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.75, B:R.293 Water bridges: B:E.289

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain B: T.192, K.374, R.375 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.192, B:T.192, B:K.374, B:R.375 Water bridges: B:T.192

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: 1 interactions with chain A, 4 interactions with chain B Metal complexes: A:D.98, B:T.56, B:F.58, B:D.60, B:S.62

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

CL.7: 5 residues within 4Å: Chain A: R.33, W.34 Chain B: N.214, V.215, W.324 Ligand excluded by PLIP

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

ACT.8: 3 residues within 4Å: Chain B: P.12, P.39, R.49 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.39 Water bridges: B:R.49 Salt bridges: B:R.49 ACT.9: 2 residues within 4Å: Chain B: M.410, R.413 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.413 ACT.10: 3 residues within 4Å: Chain B: P.191, R.195, R.375 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:P.191 Hydrogen bonds: B:R.195 Salt bridges: B:R.375, B:K.376

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

NAG.11: 6 residues within 4Å: Chain B: N.77, N.80, L.84, A.86, V.87, Q.89 6 PLIP interactions: 6 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 NAG.12: 4 residues within 4Å: Chain B: N.113, A.116, W.257, L.261 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Forbes, L.V. et al., Potent Reversible Inhibition of Myeloperoxidase by Aromatic Hydroxamates. J.Biol.Chem. (2013)

Release Date

2013-11-13

Peptides

MYELOPEROXIDASE LIGHT CHAIN: A
MYELOPEROXIDASE HEAVY CHAIN: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

MYELOPEROXIDASE LIGHT CHAIN

MYELOPEROXIDASE HEAVY CHAIN

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