SMTL ID : 5fuk.1

Crystallization of a dimeric heme peroxygenase from the fungus Marasmius rotula

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- BMA- MAN- MAN: 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.1: 4 residues within 4Å: Chain A: N.115, A.118, N.122, S.124 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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.2: 4 residues within 4Å: Chain B: N.115, A.118, N.122, S.124 No protein-ligand interaction detected (PLIP)

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

HEM.3: 24 residues within 4Å: Chain A: P.16, C.17, P.18, G.19, L.20, I.41, Y.49, L.56, A.59, G.60, L.78, I.84, E.85, H.86, S.89, L.90, S.91, R.92, E.157, F.160, V.164, F.184 Ligands: PLM.5, MG.7 27 PLIP interactions: 27 interactions with chain A, Hydrophobic interactions: A:P.18, A:L.20, A:I.41, A:I.41, A:Y.49, A:Y.49, A:A.59, A:L.78, A:I.84, A:I.84, A:F.160, A:F.160, A:F.160, A:F.160, A:V.164, A:F.184, A:F.184 Hydrogen bonds: A:H.86, A:L.90, A:S.91, A:R.92, A:E.157 Water bridges: A:H.86, A:E.157 Salt bridges: A:H.86 pi-Stacking: A:F.160 Metal complexes: A:C.17 HEM.9: 23 residues within 4Å: Chain B: P.16, C.17, P.18, G.19, L.20, I.41, Y.49, L.56, A.59, G.60, L.78, I.84, E.85, H.86, S.89, L.90, S.91, R.92, E.157, F.160, F.184 Ligands: PLM.11, MG.13 24 PLIP interactions: 24 interactions with chain B, Hydrophobic interactions: B:P.18, B:L.20, B:I.41, B:Y.49, B:L.78, B:I.84, B:I.84, B:F.160, B:F.160, B:F.184 Hydrogen bonds: B:H.86, B:L.90, B:S.91, B:R.92, B:E.157 Water bridges: B:S.89, B:S.89, B:S.89, B:S.89, B:E.157, B:E.157 Salt bridges: B:H.86 pi-Stacking: B:F.160 Metal complexes: B:C.17

2 x SNP: 1-(ISOPROPYLAMINO)-3-(1-NAPHTHYLOXY)-2-PROPANOL(Non-covalent)

SNP.4: 8 residues within 4Å: Chain A: I.55, I.62, T.152, I.153, S.156 Chain B: L.232 Ligands: PLM.5, RNP.6 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.55, A:I.62, A:I.153, A:I.153, B:L.232 SNP.10: 9 residues within 4Å: Chain B: I.55, L.58, A.59, I.62, I.84, I.153, S.156 Ligands: PLM.11, RNP.12 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.55, B:A.59, B:I.62, B:I.84, B:I.153, B:I.153 Water bridges: A:S.233

2 x PLM: PALMITIC ACID(Non-covalent)

PLM.5: 12 residues within 4Å: Chain A: I.55, L.58, A.59, I.84, T.152, S.156, E.157, F.160, I.211 Ligands: HEM.3, SNP.4, RNP.6 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.55, A:L.58, A:A.59, A:T.152, A:F.160, A:I.211 Hydrogen bonds: A:E.157 PLM.11: 9 residues within 4Å: Chain B: L.58, A.59, I.84, I.153, E.157, F.160 Ligands: HEM.9, SNP.10, RNP.12 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.58, B:A.59, B:E.157, B:F.160

2 x RNP: (1E,2R)-1-(ISOPROPYLIMINO)-3-(1-NAPHTHYLOXY)PROPAN-2-OL(Non-covalent)

RNP.6: 9 residues within 4Å: Chain A: I.55, L.58, I.62, I.153, S.156, I.211 Chain B: L.232 Ligands: SNP.4, PLM.5 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.55, A:L.58, A:I.62, A:I.153, A:I.153, B:L.232 Hydrogen bonds: A:S.156 RNP.12: 10 residues within 4Å: Chain A: L.232 Chain B: I.55, I.62, I.153, S.156, I.204, G.208, I.211 Ligands: SNP.10, PLM.11 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.62, B:I.153, B:I.153, B:I.204, A:L.232 Hydrogen bonds: B:S.156

2 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 4 residues within 4Å: Chain A: E.85, H.86, S.89 Ligands: HEM.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.85, A:H.86, A:S.89, H2O.7, H2O.7 MG.13: 4 residues within 4Å: Chain B: E.85, H.86, S.89 Ligands: HEM.9 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.85, B:H.86, B:S.89, H2O.19, H2O.19

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

NAG.8: 2 residues within 4Å: Chain A: P.142, N.143 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.143 NAG.14: 2 residues within 4Å: Chain B: N.35, S.74 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.35, B:S.74, B:S.74 Water bridges: B:N.35, B:T.72

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.15: 1 residues within 4Å: Chain B: R.185 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.181 Water bridges: B:R.185 Salt bridges: B:R.185

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Piontek, K. et al., Dimeric Heme Peroxygenase from Marasmius Rotula. To be Published

Release Date

2017-02-22

Peptides

MROUPO: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

MROUPO