SMTL ID : 3hdl.1

Crystal Structure of Highly Glycosylated Peroxidase from Royal Palm Tree

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- MAN- MAN- MAN- XYZ- FUC: alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)][beta-D-xylofuranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG-MAN-MAN-MAN-XYZ-FUC.1: 6 residues within 4Å: Chain A: Q.3, I.4, G.5, N.8, Q.118 Ligands: SO4.13 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.3, A:I.4 Hydrogen bonds: A:Q.118

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

NAG-NAG-MAN-MAN-FUC.2: 7 residues within 4Å: Chain A: N.28, N.29, F.77 Ligands: SO4.11, SO4.12, EDO.30, EDO.31 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.56, A:K.65, A:L.74

2 x NAG- FUC- NAG: alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Non-functional Binders)

NAG-FUC-NAG.3: 3 residues within 4Å: Chain A: N.144, Q.147 Ligands: SO4.18 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.150 NAG-FUC-NAG.4: 2 residues within 4Å: Chain A: N.211 Ligands: SO4.17 No protein-ligand interaction detected (PLIP)

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.5: 4 residues within 4Å: Chain A: N.267, T.269, A.270 Ligands: SO4.16 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- MAN- MAN- MAN- FUC: alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)

NAG-NAG-MAN-MAN-MAN-FUC.6: 4 residues within 4Å: Chain A: D.56, N.298, S.300, V.301 No protein-ligand interaction detected (PLIP)

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

HEM.7: 26 residues within 4Å: Chain A: P.34, G.35, I.37, R.38, F.41, S.73, R.75, P.139, S.140, P.141, L.148, F.152, L.165, S.166, A.168, H.169, G.172, V.173, A.174, H.175, S.178, L.222, L.245, S.247, M.279 Ligands: PEO.10 29 PLIP interactions: 29 interactions with chain A, Hydrophobic interactions: A:P.34, A:I.37, A:R.38, A:F.41, A:F.41, A:F.41, A:P.141, A:L.148, A:F.152, A:F.152, A:L.165, A:L.165, A:A.168, A:A.174, A:L.222 Hydrogen bonds: A:V.173, A:V.173, A:H.175, A:S.178 Water bridges: A:R.38, A:S.73, A:V.173, A:H.175 Salt bridges: A:R.38, A:R.75, A:H.175 pi-Stacking: A:F.41 pi-Cation interactions: A:R.38 Metal complexes: A:H.169

2 x CA: CALCIUM ION(Non-covalent)

CA.8: 5 residues within 4Å: Chain A: S.170, D.223, T.226, V.229, D.231 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:S.170, A:S.170, A:D.223, A:T.226, A:V.229 CA.9: 5 residues within 4Å: Chain A: D.43, V.46, G.48, D.50, S.52 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.43, A:V.46, A:G.48, A:S.52, H2O.10

1 x PEO: HYDROGEN PEROXIDE(Non-functional Binders)

PEO.10: 4 residues within 4Å: Chain A: R.38, F.41, H.42 Ligands: HEM.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.38, A:H.42

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

SO4.11: 4 residues within 4Å: Ligands: NAG-NAG-MAN-MAN-FUC.2, NAG-NAG-MAN-MAN-FUC.2, NAG-NAG-MAN-MAN-FUC.2, SO4.12 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.29 SO4.12: 7 residues within 4Å: Chain A: R.75, G.76, F.77, E.78 Ligands: NAG-NAG-MAN-MAN-FUC.2, SO4.11, EDO.31 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.76, A:F.77, A:E.78 SO4.13: 3 residues within 4Å: Ligands: NAG-NAG-MAN-MAN-MAN-XYZ-FUC.1, NAG-NAG-MAN-MAN-MAN-XYZ-FUC.1, NAG-NAG-MAN-MAN-MAN-XYZ-FUC.1 No protein-ligand interaction detected (PLIP) SO4.14: 5 residues within 4Å: Chain A: I.225, T.226, P.227, S.228, V.229 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.228, A:V.229 SO4.15: 2 residues within 4Å: Chain A: Y.117, Q.118 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.118, A:Q.118 SO4.16: 3 residues within 4Å: Chain A: S.273 Ligands: NAG-NAG.5, NAG-NAG.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.273, A:S.273 Water bridges: A:Q.277 SO4.17: 2 residues within 4Å: Ligands: NAG-FUC-NAG.4, NAG-FUC-NAG.4 No protein-ligand interaction detected (PLIP) SO4.18: 2 residues within 4Å: Ligands: NAG-FUC-NAG.3, NAG-FUC-NAG.3 No protein-ligand interaction detected (PLIP)

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.19: 5 residues within 4Å: Chain A: P.141, S.177, T.213, R.214 Ligands: EDO.28 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.214

16 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.20: 2 residues within 4Å: Chain A: V.220, S.221 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain A: Q.277, V.280, K.281, Q.284 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain A: N.232, A.265, M.266, N.267, L.268 Ligand excluded by PLIP EDO.23: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain A: T.180, N.181, Y.184, N.185 Ligand excluded by PLIP EDO.25: 1 residues within 4Å: Chain A: R.47 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain A: G.113, N.114, L.268, A.272 Ligands: EDO.33 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain A: T.62, D.66, I.68, A.131, N.135 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain A: T.213, R.214, F.215 Ligands: MES.19 Ligand excluded by PLIP EDO.29: 4 residues within 4Å: Chain A: Y.184, N.185, G.191, R.205 Ligand excluded by PLIP EDO.30: 7 residues within 4Å: Chain A: N.70, N.71, P.72, S.73, L.74, F.77 Ligands: NAG-NAG-MAN-MAN-FUC.2 Ligand excluded by PLIP EDO.31: 6 residues within 4Å: Chain A: D.56, K.65, F.77, S.300 Ligands: NAG-NAG-MAN-MAN-FUC.2, SO4.12 Ligand excluded by PLIP EDO.32: 8 residues within 4Å: Chain A: G.5, F.6, Y.7, N.8, C.11, P.12, A.14, E.15 Ligand excluded by PLIP EDO.33: 7 residues within 4Å: Chain A: N.114, I.115, T.116, A.272, S.273, A.276 Ligands: EDO.26 Ligand excluded by PLIP EDO.34: 8 residues within 4Å: Chain A: G.31, P.34, R.75, I.171, G.172, V.173, P.227, S.228 Ligand excluded by PLIP EDO.35: 3 residues within 4Å: Chain A: T.158, D.160, E.161 Ligand excluded by PLIP

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

NAG.36: 2 residues within 4Å: Chain A: A.153, N.154 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.155 NAG.37: 1 residues within 4Å: Chain A: N.114 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.114 Water bridges: A:N.114 NAG.38: 1 residues within 4Å: Chain A: N.256 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.256 Water bridges: A:N.256, A:N.256, A:N.256

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Watanabe, L. et al., Crystal structure and statistical coupling analysis of highly glycosylated peroxidase from royal palm tree (Roystonea regia). J.Struct.Biol. (2010)

Release Date

2009-11-24

Peptides

Royal Palm Tree Peroxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Royal Palm Tree Peroxidase