SMTL ID : 1mhl.1 (2 other biounits)

CRYSTAL STRUCTURE OF HUMAN MYELOPEROXIDASE ISOFORM C CRYSTALLIZED IN SPACE GROUP P2(1) AT PH 5.5 AND 20 DEG C

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 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

NAG-NAG-BMA-MAN-MAN-FUC.1: 16 residues within 4Å: Chain B: N.205, S.207, V.208, R.392 Chain C: W.34, L.35 Chain D: K.196, Y.197, R.326, F.327, C.328, G.329, T.389, K.393 Ligands: NAG-NAG-BMA-MAN-MAN-FUC.2, NAG-NAG-BMA-MAN-MAN-FUC.2 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B, 1 interactions with chain C Water bridges: D:K.196, B:S.207 Hydrophobic interactions: B:V.208, B:R.392, C:L.35 Hydrogen bonds: D:K.393 NAG-NAG-BMA-MAN-MAN-FUC.2: 16 residues within 4Å: Chain A: W.34, L.35 Chain B: K.196, Y.197, R.326, F.327, C.328, G.329, T.389, 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 B, 1 interactions with chain D, 1 interactions with chain A Water bridges: B:K.196, B:K.196, D:R.392, D:S.207 Hydrophobic interactions: D:V.208, D:R.392, A:L.35 Hydrogen bonds: B:K.393

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

NAG.3: 6 residues within 4Å: Chain B: N.77, N.80, L.84, A.86, V.87, Q.89 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.80, B:V.87, B:Q.89, B:Q.89 Water bridges: B:N.77 NAG.4: 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 NAG.8: 7 residues within 4Å: Chain D: N.77, N.80, L.82, L.84, A.86, V.87, Q.89 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:N.80, D:V.87, D:Q.89, D:Q.89 Water bridges: D:N.77, D:N.77 NAG.9: 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.5: 5 residues within 4Å: Chain A: D.98 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 CA.10: 5 residues within 4Å: Chain C: D.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.98, C:D.98, D:T.56, D:F.58, D:S.62

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

CL.6: 5 residues within 4Å: Chain A: R.33, W.34 Chain B: N.214, V.215, W.324 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain C: R.33, W.34 Chain D: N.214, V.215, W.324 Ligand excluded by PLIP

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.7: 21 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, T.217, F.220, R.221, G.223, H.224, I.227, F.253, L.294, F.295, L.305, R.312 24 PLIP interactions: 19 interactions with chain B, 5 interactions with chain A, Hydrophobic interactions: B:E.130, B:M.131, B:R.221, B:I.227, B:F.253, B:L.294, B:F.295, B:L.305, B:L.305, A:Q.93, A:Q.93 Water bridges: B:R.127, B:R.127, B:R.221, 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 Hydrogen bonds: A:D.100, A:T.102, A:T.102 HEM.12: 22 residues within 4Å: Chain C: M.89, G.92, Q.93, D.96, D.100, F.101, T.102 Chain D: R.127, E.130, M.131, T.217, F.220, R.221, G.223, H.224, I.227, F.253, L.294, F.295, L.305, L.308, R.312 20 PLIP interactions: 16 interactions with chain D, 4 interactions with chain C, Hydrophobic interactions: D:E.130, 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.93, C:Q.93 Water bridges: D:R.221, D:R.221, D:R.221 Salt bridges: D:R.127, D:R.221, D:R.312 Metal complexes: D:H.224 Hydrogen bonds: C:D.100, C:T.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fenna, R. et al., Structure of the green heme in myeloperoxidase. Arch.Biochem.Biophys. (1995)

Release Date

1996-01-06

Peptides

MYELOPEROXIDASE: AC
MYELOPEROXIDASE: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

B
C

D
D

MYELOPEROXIDASE

MYELOPEROXIDASE

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