SMTL ID : 5fuj.1

Crystallization of a dimeric heme peroxygenase from the fungus Marasmius rotula

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

homo-dimer

Ligands

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

NAG-NAG.1: 3 residues within 4Å: Chain A: R.34, N.35, S.74 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(Non-functional Binders)

NAG-NAG-BMA.2: 5 residues within 4Å: Chain A: N.115, P.116, A.118, N.122, S.124 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-MAN.3: 5 residues within 4Å: Chain B: N.115, P.116, A.118, N.122, S.124 No protein-ligand interaction detected (PLIP)

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

HEM.4: 23 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, F.184 Ligands: ACT.5, MG.6 31 PLIP interactions: 30 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:P.18, A:L.20, A:I.41, A:Y.49, A:Y.49, A:A.59, A:L.78, A:I.84, A:I.84, A:E.157, A:E.157, A:F.160, A:F.160, A:F.160, A:F.184 Hydrogen bonds: A:E.85, A:H.86, A:L.90, A:S.91, A:R.92, A:E.157 Water bridges: A:H.86, A:S.89, A:S.89, A:S.89, A:S.89, A:E.157 Salt bridges: A:H.86 pi-Stacking: A:F.160 Metal complexes: A:C.17, ACT.5 HEM.8: 24 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, G.63, L.78, I.84, E.85, H.86, S.89, L.90, S.91, R.92, E.157, F.160, F.184 Ligands: ACT.9, MG.10 26 PLIP interactions: 25 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:P.18, B:L.20, B:I.41, B:Y.49, B:L.78, B:L.78, B:I.84, B:I.84, B:F.160, B:F.160, B:F.160, B:F.184, B:F.184 Hydrogen bonds: B:H.86, B:L.90, B:S.91, B:R.92 Water bridges: B:S.89, B:S.89, B:S.89, B:S.89, B:E.157 Salt bridges: B:H.86 pi-Stacking: B:F.160 Metal complexes: B:C.17, ACT.9

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

ACT.5: 5 residues within 4Å: Chain A: A.59, I.84, E.157, F.160 Ligands: HEM.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.59, A:F.160 ACT.9: 6 residues within 4Å: Chain B: A.59, I.84, I.153, E.157, F.160 Ligands: HEM.8 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.59, B:F.160 Hydrogen bonds: B:E.157 ACT.11: 5 residues within 4Å: Chain B: E.93, N.104, A.106, I.107, R.140 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.104 Water bridges: B:E.93, B:R.140

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 4 residues within 4Å: Chain A: E.85, H.86, S.89 Ligands: HEM.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.85, A:H.86, A:S.89, H2O.5, H2O.5 MG.10: 4 residues within 4Å: Chain B: E.85, H.86, S.89 Ligands: HEM.8 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.85, B:H.86, B:S.89, H2O.16, H2O.16

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: W.5, F.103, F.184, R.185, E.186, E.187 3 PLIP interactions: 3 interactions with chain A Water bridges: A:F.103, A:E.187, A:E.187

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Piontek, K. et al., Crystallization of a Dimeric Heme Peroxygenase. To be Published

Release Date

2017-02-22

Peptides

MROUPO: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

MROUPO