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

STRUCTURAL ANALYSES OF HUMAN MYELOPEROXIDASE-THIOCYANATE COMPLEX

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 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: 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: 15 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: R.202, 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, 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: D:V.208, A:L.33 Hydrogen bonds: B:K.393 Water bridges: B:K.393, D:S.207

4 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.3: 8 residues within 4Å: Chain A: V.30, R.31, W.32, L.33 Chain B: N.214, V.215, L.318, W.324 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:W.32, B:N.214, B:V.215 SCN.5: 5 residues within 4Å: Chain A: Q.91, H.95 Chain B: R.127, E.130 Ligands: HEM.10 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.91 Water bridges: B:R.127, B:R.127 SCN.14: 8 residues within 4Å: Chain C: R.31, W.32, L.33 Chain D: N.214, V.215, L.318, P.319, W.324 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:N.214, D:V.215, C:W.32 SCN.15: 5 residues within 4Å: Chain C: Q.91, H.95 Chain D: R.127, E.130 Ligands: HEM.16 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Water bridges: D:R.127, D:R.127 Hydrogen bonds: C:Q.91

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

SO4.4: 3 residues within 4Å: Chain A: T.73 Chain B: D.288, R.293 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Water bridges: B:D.288, B:R.293, B:R.293, B:R.293, B:R.293, A:T.73, A:T.73 Salt bridges: B:R.293 Hydrogen bonds: A:T.73, A:T.73 SO4.9: 1 residues within 4Å: Chain B: R.117 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.117 SO4.20: 3 residues within 4Å: Chain C: T.73 Chain D: D.288, R.293 9 PLIP interactions: 6 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:E.289, C:T.73 Water bridges: D:D.288, D:R.293, D:R.293, D:R.293, C:T.73, C:T.73 Salt bridges: D:R.293

4 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 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.7: 4 residues within 4Å: Chain B: N.113, A.116, W.257, L.261 No protein-ligand interaction detected (PLIP) NAG.17: 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 Hydrogen bonds: D:N.80, D:V.87, D:Q.89, D:Q.89 Water bridges: D:N.77, D:N.77 NAG.18: 4 residues within 4Å: Chain D: N.113, S.115, A.116, W.257 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.113 Water bridges: D:N.244

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: 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.19: 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:F.58, D:D.60, D:S.62, C:D.96

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.10: 23 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, F.295, L.305, L.308, R.312 Ligands: SCN.5 24 PLIP interactions: 17 interactions with chain B, 7 interactions with chain A, 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, A:Q.91, A:Q.91 Water bridges: B:R.127, B:R.221, B:R.221, B:R.221, B:R.221, A:E.102 Salt bridges: B:R.127, B:R.221, B:R.312 Metal complexes: B:H.224 Hydrogen bonds: A:D.98, A:D.98, A:T.100, A:T.100 HEM.16: 24 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, L.294, F.295, L.305, L.308, R.312 Ligands: SCN.15 24 PLIP interactions: 18 interactions with chain D, 6 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: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, D:R.221, D:R.221, C:E.102 Salt bridges: D:R.127, D:R.221, D:R.312 Metal complexes: D:H.224 Hydrogen bonds: C:D.98, C:D.98, C:T.100

6 x ACY: ACETIC ACID(Non-functional Binders)

ACY.11: 4 residues within 4Å: Chain B: P.11, P.12, R.36, R.49 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.11 Water bridges: B:R.49 Salt bridges: B:R.49 ACY.12: 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 ACY.13: 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 ACY.21: 3 residues within 4Å: Chain D: P.12, R.36, R.49 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:P.12 Water bridges: D:S.37, D:R.49 Salt bridges: D:R.36, D:R.49 ACY.22: 2 residues within 4Å: Chain D: M.410, R.413 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.413 ACY.23: 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

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

2001-12-21

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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