SMTL ID : 1d7w.1 (2 other biounits)

CRYSTAL STRUCTURE OF HUMAN MYELOPEROXIDASE ISOFORM C COMPLEXED WITH CYANIDE AND BROMIDE AT PH 4.0

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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(Post Translational Modification)

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 C, 1 interactions with chain D Hydrophobic interactions: B:V.208, C:L.33 Hydrogen bonds: C:W.32, 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 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: D:V.208, A:L.33 Hydrogen bonds: D:R.392, A:W.32, B:K.393 Water bridges: D:K.393, B:G.329, B:G.329, D:S.207

8 x BR: BROMIDE ION(Non-covalent)

BR.3: 5 residues within 4Å: Chain A: R.31, W.32 Chain B: N.214, V.215, W.324 Ligand excluded by PLIP BR.18: 5 residues within 4Å: Chain B: N.236, R.270, I.431, T.432, T.433 Ligand excluded by PLIP BR.19: 4 residues within 4Å: Chain B: N.88, Q.89, P.100, F.101 Ligand excluded by PLIP BR.20: 2 residues within 4Å: Chain B: R.127, E.130 Ligand excluded by PLIP BR.22: 5 residues within 4Å: Chain C: R.31, W.32 Chain D: N.214, V.215, W.324 Ligand excluded by PLIP BR.35: 5 residues within 4Å: Chain D: N.236, R.270, I.431, T.432, T.433 Ligand excluded by PLIP BR.36: 4 residues within 4Å: Chain D: N.88, Q.89, P.100, F.101 Ligand excluded by PLIP BR.37: 2 residues within 4Å: Chain D: R.127, E.130 Ligand excluded by PLIP

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

SO4.4: 3 residues within 4Å: Chain A: T.73 Chain B: D.288, R.293 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:T.73, A:T.73 Water bridges: A:T.73, A:T.73, B:D.288, B:R.293, B:R.293, B:R.293 Salt bridges: B:R.293 SO4.11: 1 residues within 4Å: Chain B: R.117 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.117 SO4.12: 3 residues within 4Å: Chain A: E.81 Chain B: K.376, R.378 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.376 Water bridges: B:R.378, A:R.82, A:R.82 Salt bridges: B:R.378 SO4.23: 2 residues within 4Å: Chain C: T.73 Chain D: R.293 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:T.73 Water bridges: C:T.73, C:T.73, D:R.293, D:R.293, D:R.293 Salt bridges: D:R.293 SO4.30: 3 residues within 4Å: Chain C: E.81 Chain D: K.376, R.378 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:K.376 Water bridges: D:G.377, D:R.378, D:R.378, C:R.82 Salt bridges: D:R.378

2 x CYN: CYANIDE ION(Non-covalent)

CYN.5: 3 residues within 4Å: Chain A: Q.91, H.95 Ligands: HEM.7 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:R.127 Hydrogen bonds: A:Q.91, A:H.95 CYN.25: 3 residues within 4Å: Chain C: Q.91, H.95 Ligands: HEM.26 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Water bridges: D:R.127 Hydrogen bonds: C:Q.91, C:H.95

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

ACT.6: 8 residues within 4Å: Chain A: N.16, S.19, L.22 Chain B: D.206, S.207, V.208, D.209 Chain C: P.34 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.22 Hydrogen bonds: A:N.16 Water bridges: A:R.18, A:R.18, A:R.18, B:S.207 Salt bridges: A:R.18 ACT.13: 4 residues within 4Å: Chain B: P.11, P.12, R.36, R.49 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.11 Salt bridges: B:R.49 ACT.14: 2 residues within 4Å: Chain B: M.410, R.413 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.410 Salt bridges: B:R.413 ACT.15: 3 residues within 4Å: Chain B: P.191, R.195, R.375 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.191 Salt bridges: B:R.195, B:R.375 ACT.16: 7 residues within 4Å: Chain B: M.175, I.419, S.420, R.423, I.424, D.427, L.458 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:R.423, B:I.424 Hydrogen bonds: B:S.420, B:I.424 Water bridges: B:D.427, B:L.458 ACT.17: 1 residues within 4Å: Chain B: N.459 No protein-ligand interaction detected (PLIP) ACT.21: 6 residues within 4Å: Chain A: P.34 Chain C: N.16, S.19, L.22 Chain D: D.206, S.207 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:L.22 Hydrogen bonds: C:N.16 Water bridges: C:R.18, C:R.18, A:E.36 Salt bridges: C:R.18 ACT.24: 4 residues within 4Å: Chain A: N.54 Chain C: C.1, P.2, R.17 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.17 ACT.31: 3 residues within 4Å: Chain D: P.12, R.36, R.49 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:P.12 Water bridges: D:R.36, D:R.36, D:R.49 Salt bridges: D:R.36, D:R.49 ACT.32: 2 residues within 4Å: Chain D: M.410, R.413 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:M.410 Salt bridges: D:R.413 ACT.33: 4 residues within 4Å: Chain D: P.191, R.195, R.375, K.376 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:P.191 Salt bridges: D:R.195, D:R.375, D:K.376 ACT.34: 10 residues within 4Å: Chain D: M.175, Q.418, I.419, S.420, R.423, I.424, D.427, P.456, A.457, L.458 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:I.419, D:R.423, D:I.424 Hydrogen bonds: D:S.420, D:I.424 Water bridges: D:D.427, D:L.458

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.7: 24 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, 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: CYN.5 24 PLIP interactions: 5 interactions with chain A, 19 interactions with chain B, Hydrophobic interactions: A:Q.91, A:Q.91, B:E.130, B:M.131, B:F.220, B:F.220, B:R.221, B:I.227, B:F.253, B:L.294, B:F.295, B:L.305, B:L.305 Hydrogen bonds: A:D.98, A:T.100, A:T.100 Water bridges: 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 HEM.26: 23 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, G.223, H.224, I.227, F.253, F.295, L.305, L.308, R.312 Ligands: CYN.25 20 PLIP interactions: 16 interactions with chain D, 4 interactions with chain C, Hydrophobic interactions: D:E.130, D:M.131, D:F.220, D:R.221, D:I.227, D:F.253, D:F.295, D:L.305, D:L.305, C:Q.91, C:Q.91 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.98, C:T.100

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

NAG.8: 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:N.77 NAG.9: 5 residues within 4Å: Chain B: N.113, S.115, A.116, W.257, L.261 No protein-ligand interaction detected (PLIP) NAG.27: 6 residues within 4Å: Chain D: N.77, N.80, L.84, A.86, V.87, Q.89 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:A.86 Hydrogen bonds: D:N.80, D:V.87, D:Q.89, D:Q.89 Water bridges: D:N.77 NAG.28: 4 residues within 4Å: Chain D: N.113, 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.10: 5 residues within 4Å: Chain A: D.96 Chain B: T.56, F.58, D.60, S.62 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Metal complexes: B:T.56, B:F.58, B:S.62, A:D.96, A:D.96 CA.29: 5 residues within 4Å: Chain C: D.96 Chain D: T.56, F.58, D.60, S.62 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Metal complexes: D:T.56, D:T.56, D:F.58, D:S.62, C:D.96

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Blair-Johnson, M. et al., Human myeloperoxidase: structure of a cyanide complex and its interaction with bromide and thiocyanate substrates at 1.9 A resolution. Biochemistry (2001)

Release Date

2001-12-12

Peptides

MYELOPEROXIDASE: AC
MYELOPEROXIDASE: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

B
C

D
D

MYELOPEROXIDASE

MYELOPEROXIDASE

Related Entries With Identical Sequence