SMTL ID : 5aog.1

Structure of Sorghum peroxidase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.27 Å

Oligo State

monomer

Ligands

1 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)

NAG-FUC-NAG.1: 4 residues within 4Å: Chain A: D.62, N.299, S.301, A.302 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.62

1 x NAG- NAG- BMA- XYP- MAN- FUC: beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)]beta-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-BMA-XYP-MAN-FUC.2: 4 residues within 4Å: Chain A: N.201, T.203, N.241, E.243 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.241 Water bridges: A:N.241

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

HEM.3: 26 residues within 4Å: Chain A: A.40, G.41, L.43, R.44, F.47, P.75, N.76, R.80, P.148, P.149, P.150, L.174, G.177, H.178, I.180, G.181, L.182, G.183, H.184, S.187, R.220, L.223, F.246, S.248 Ligands: GOL.6, IAC.7 24 PLIP interactions: 24 interactions with chain A, Hydrophobic interactions: A:L.43, A:R.44, A:R.44, A:F.47, A:F.47, A:F.47, A:N.76, A:P.148, A:P.150, A:L.174, A:L.223, A:F.246, A:F.246 Hydrogen bonds: A:L.182, A:H.184, A:S.187 Water bridges: A:R.44, A:R.44, A:P.75, A:N.76 Salt bridges: A:R.80, A:R.220 pi-Stacking: A:F.47 Metal complexes: A:H.178

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain A: T.179, D.224, T.227, A.230, D.232 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.179, A:T.179, A:D.224, A:T.227, A:A.230

1 x NA: SODIUM ION(Non-functional Binders)

NA.5: 5 residues within 4Å: Chain A: D.49, V.52, G.54, D.56, S.58 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.54, A:D.56, A:D.56, A:S.58

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 8 residues within 4Å: Chain A: R.44, F.47, N.76, L.77, P.148, P.149, P.150 Ligands: HEM.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.76 Water bridges: A:R.44, A:R.44

1 x IAC: 1H-INDOL-3-YLACETIC ACID(Non-covalent)

IAC.7: 7 residues within 4Å: Chain A: T.78, L.79, R.80, P.81, L.182, R.220 Ligands: HEM.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:R.80, A:L.182 Hydrogen bonds: A:T.78 Salt bridges: A:R.220 pi-Cation interactions: A:R.220, A:R.220

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nnamchi, C.I. et al., Structural and Spectroscopic Characterisation of a Heme Peroxidase from Sorghum. J.Biol.Inorg.Chem. (2016)

Release Date

2016-01-13

Peptides

CATIONIC PEROXIDASE SPC4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

CATIONIC PEROXIDASE SPC4