SMTL ID : 2yp1.1 (1 other biounit)

Crystallization of a 45 kDa peroxygenase- peroxidase from the mushroom Agrocybe aegerita and structure determination by SAD utilizing only the haem iron

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG-BMA-MAN-MAN-MAN.1: 6 residues within 4Å: Chain A: F.130, F.131, N.138, L.141, T.176, P.178 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.176

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG-BMA-MAN-MAN.2: 13 residues within 4Å: Chain A: F.152, G.153, G.154, N.158, T.160, Q.210 Chain B: C.275, L.276, E.279, A.314, C.316, T.317 Ligands: SO4.23 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.279, B:C.275 Water bridges: B:E.279

5 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 2 residues within 4Å: Chain A: F.130, N.179 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain A: N.8, S.10, A.11, K.12 Chain B: E.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.10 Water bridges: A:A.11 NAG-NAG.7: 13 residues within 4Å: Chain A: C.275, L.276, E.279, A.314, C.316, T.317 Chain B: F.152, G.153, G.154, N.158, T.160, Q.210 Ligands: SO4.16 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.317 NAG-NAG.8: 6 residues within 4Å: Chain B: N.283, K.287, V.319, F.320, P.321, G.323 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain A: E.7 Chain B: N.8, S.10, A.11, K.12 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.4: 6 residues within 4Å: Chain A: E.279, N.283, K.287, F.320, P.321, G.323 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.6: 4 residues within 4Å: Chain B: N.138, T.140, L.141 Ligands: SO4.24 No protein-ligand interaction detected (PLIP)

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.10: 28 residues within 4Å: Chain A: P.32, C.33, P.34, G.35, L.36, I.56, V.60, F.66, A.71, A.74, T.75, A.78, L.112, F.118, E.119, G.120, S.123, M.124, T.125, R.126, R.186, E.193, F.196, P.197, L.200, F.201 Ligands: MG.11, ACT.12 29 PLIP interactions: 28 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:P.32, A:P.34, A:L.36, A:L.36, A:I.56, A:V.60, A:F.66, A:F.66, A:A.74, A:A.78, A:F.118, A:F.118, A:F.196, A:F.196, A:P.197, A:L.200, A:F.201 Hydrogen bonds: A:S.123, A:M.124, A:T.125, A:T.125, A:R.126, A:E.193 Water bridges: A:R.166, A:R.186 Salt bridges: A:R.186 pi-Stacking: A:F.196 Metal complexes: A:C.33, ACT.12 HEM.17: 28 residues within 4Å: Chain B: P.32, C.33, P.34, G.35, L.36, I.56, V.60, L.64, F.66, A.71, A.74, T.75, A.78, F.118, E.119, G.120, S.123, M.124, T.125, R.186, E.193, F.196, P.197, L.200, F.201, F.220 Ligands: MG.18, ACT.20 29 PLIP interactions: 28 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:P.32, B:P.34, B:L.36, B:I.56, B:L.64, B:F.66, B:A.74, B:A.78, B:F.118, B:F.118, B:E.193, B:F.196, B:P.197, B:L.200, B:F.201 Hydrogen bonds: B:G.120, B:M.124, B:T.125, B:T.125, B:R.126 Water bridges: B:S.123, B:S.123, B:S.123, B:E.193, B:E.193 Salt bridges: B:R.186 pi-Stacking: B:F.196 Metal complexes: B:C.33, ACT.20

2 x MG: MAGNESIUM ION(Non-covalent)

MG.11: 4 residues within 4Å: Chain A: E.119, G.120, S.123 Ligands: HEM.10 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.119, A:G.120, A:S.123, H2O.5, H2O.5 MG.18: 4 residues within 4Å: Chain B: E.119, G.120, S.123 Ligands: HEM.17 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.119, B:G.120, B:S.123, H2O.18, H2O.18

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

ACT.12: 7 residues within 4Å: Chain A: F.66, A.74, F.118, T.189, E.193, F.196 Ligands: HEM.10 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.66, A:A.74, A:F.196 Hydrogen bonds: A:E.193 ACT.20: 6 residues within 4Å: Chain B: A.74, F.118, T.189, E.193, F.196 Ligands: HEM.17 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.74, B:F.196 ACT.25: 3 residues within 4Å: Chain B: R.97, L.98, G.100 No protein-ligand interaction detected (PLIP)

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

SO4.13: 4 residues within 4Å: Chain A: R.94, K.95, T.96, R.97 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.96, A:R.97 Water bridges: A:R.94 Salt bridges: A:R.94, A:R.97 SO4.14: 2 residues within 4Å: Chain A: R.94, H.135 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.30, A:R.94 Salt bridges: A:R.94, A:H.135 SO4.15: 3 residues within 4Å: Chain A: Y.148, R.151, K.168 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.151, A:K.168 SO4.16: 7 residues within 4Å: Chain A: T.273, P.274, C.275, L.276 Chain B: T.160 Ligands: NAG-NAG.7, NAG-NAG.7 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:C.275, A:L.276, B:T.160 SO4.21: 3 residues within 4Å: Chain B: R.94, T.96, R.97 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.96, B:R.97 Salt bridges: B:R.94, B:R.97 SO4.22: 2 residues within 4Å: Chain B: R.94, H.135 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.94, B:N.113, B:H.135 Salt bridges: B:R.94, B:H.135 SO4.23: 8 residues within 4Å: Chain A: T.160 Chain B: S.272, T.273, P.274, C.275, L.276 Ligands: NAG-NAG-BMA-MAN-MAN.2, NAG-NAG-BMA-MAN-MAN.2 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:C.275, B:L.276, A:T.160 SO4.24: 4 residues within 4Å: Chain B: N.138, E.139, T.140 Ligands: NAG-NAG-BMA.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.139, B:T.140, B:T.140

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

NAG.19: 2 residues within 4Å: Chain B: F.130, N.179 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.130 Hydrogen bonds: B:N.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Piontek, K. et al., Structural Basis of Substrate Conversion in a New Aromatic Peroxygenase: P450 Functionality with Benefits. J.Biol.Chem. (2013)

Release Date

2013-10-23

Peptides

AROMATIC PEROXYGENASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

AROMATIC PEROXYGENASE

Related Entries With Identical Sequence