SMTL ID : 4a5g.1 (1 other biounit)

Raphanus sativus anionic peroxidase.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

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.1: 4 residues within 4Å: Chain A: N.5, T.7, F.8 Ligands: 1PE.12 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.8

1 x NAG- NAG- BMA- FUC: 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-FUC.2: 6 residues within 4Å: Chain A: N.68, G.70, A.73, Q.133, A.134, N.137 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.73

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

NAG-NAG-MAN-FUL.3: 5 residues within 4Å: Chain A: N.199, Q.239, S.240, N.241, N.242 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.240

1 x NAG- NAG- MAN- FUC: 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

NAG-NAG-MAN-FUC.4: 4 residues within 4Å: Chain A: N.269, T.271, L.272, Q.275 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.275

1 x NAG- NAG- BMA- XYP- BMA- FUL: beta-D-xylopyranose-(1-2)-[beta-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-XYP-BMA-FUL.5: 3 residues within 4Å: Chain A: N.187, G.190, G.192 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.6: 3 residues within 4Å: Chain A: N.15, A.18, T.22 No protein-ligand interaction detected (PLIP)

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

HEM.7: 28 residues within 4Å: Chain A: R.33, A.36, S.37, I.39, R.40, F.43, S.75, R.77, P.141, S.142, P.143, F.154, L.164, L.167, S.168, A.170, H.171, F.173, G.174, R.175, A.176, T.177, V.180, L.222, L.245, S.247, M.281, M.284 30 PLIP interactions: 30 interactions with chain A, Hydrophobic interactions: A:A.36, A:I.39, A:R.40, A:F.43, A:F.43, A:F.43, A:P.141, A:P.143, A:F.154, A:L.164, A:L.167, A:A.170, A:F.173, A:A.176, A:V.180, A:L.222 Hydrogen bonds: A:R.175, A:R.175, A:T.177 Water bridges: A:R.33, A:R.33, A:S.75, A:R.77, A:T.177, A:T.177 Salt bridges: A:R.33, A:R.40 pi-Stacking: A:F.43 pi-Cation interactions: A:R.40 Metal complexes: A:H.171

2 x CA: CALCIUM ION(Non-covalent)

CA.8: 5 residues within 4Å: Chain A: D.45, V.48, G.50, D.52, S.54 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.45, A:V.48, A:G.50, A:D.52, A:S.54 CA.9: 5 residues within 4Å: Chain A: T.172, D.223, T.226, A.229, D.231 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.172, A:T.172, A:D.223, A:T.226, A:A.229

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

NAG.10: 2 residues within 4Å: Chain A: Q.145, N.149 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.145

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.11: 5 residues within 4Å: Chain A: G.2, S.3, L.4, N.286, P.289 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.2, A:S.3, A:L.4 1PE.12: 3 residues within 4Å: Chain A: G.292, S.293 Ligands: NAG-NAG-BMA-XYP-MAN-FUC.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gil-Rodriguez, P. et al., Crystallographic Structure of the Raphanus Sativus Anionic Peroxidase. To be Published

Release Date

2012-11-07

Peptides

ANIONIC PEROXIDASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ANIONIC PEROXIDASE

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