SMTL ID : 2j5m.1

Structure of Chloroperoxidase Compound 0

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

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

NAG-NAG-BMA.1: 9 residues within 4Å: Chain A: S.26, R.47, V.83, N.94, T.96, P.279, F.280, L.281, L.282 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.279 Hydrogen bonds: A:L.282

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.2: 9 residues within 4Å: Chain A: K.212, Y.213, T.216, N.217, H.223, L.224, P.293, L.295, D.299 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.293

1 x MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose(Post Translational Modification)

MAN-MAN.3: 3 residues within 4Å: Chain A: T.284, N.285, A.286 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.285 Water bridges: A:T.284, A:A.286

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.4: 4 residues within 4Å: Chain A: E.105, H.106, S.109 Ligands: HEM.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.105, A:H.106, A:S.109, H2O.13, H2O.13

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

HEM.5: 26 residues within 4Å: Chain A: P.29, C.30, P.31, A.32, L.33, F.58, I.64, I.69, A.72, L.73, A.76, L.98, F.104, E.105, H.106, S.109, F.110, S.111, R.112, E.184, F.187, I.188, W.214, F.215 Ligands: MN.4, PEO.6 34 PLIP interactions: 34 interactions with chain A, Hydrophobic interactions: A:P.29, A:P.31, A:A.32, A:L.33, A:F.58, A:F.58, A:F.58, A:I.64, A:I.64, A:I.69, A:A.72, A:L.73, A:A.76, A:L.98, A:F.104, A:F.104, A:F.104, A:F.104, A:E.184, A:F.187, A:F.187, A:I.188, A:W.214, A:F.215 Hydrogen bonds: A:H.106, A:F.110, A:S.111, A:R.112, A:E.184 Water bridges: A:Q.181, A:E.184 Salt bridges: A:H.106 pi-Stacking: A:F.187 Metal complexes: A:C.30

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

PEO.6: 4 residues within 4Å: Chain A: F.104, E.184, F.187 Ligands: HEM.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.184

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

NAG.7: 4 residues within 4Å: Chain A: Y.9, P.10, Y.11, N.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.10, A:N.13

10 x MAN: alpha-D-mannopyranose(Post Translational Modification)

MAN.8: 5 residues within 4Å: Chain A: E.236, T.239, S.240, E.267 Ligands: MAN.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.267 MAN.9: 7 residues within 4Å: Chain A: Y.151, D.201, E.202, P.204, F.237, S.240 Ligands: MAN.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.151, A:E.202 Water bridges: A:D.201, A:D.201 MAN.10: 11 residues within 4Å: Chain A: P.179, N.182, V.183, T.239, S.242, S.243, L.246, G.265, A.266, A.268 Ligands: MAN.8 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:P.179, A:V.183, A:G.265, A:A.268 Water bridges: A:G.265, A:E.267 MAN.11: 5 residues within 4Å: Chain A: S.240, S.243, A.244, A.247 Ligands: MAN.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.240 MAN.12: 3 residues within 4Å: Chain A: S.249, V.250, T.251 No protein-ligand interaction detected (PLIP) MAN.13: 6 residues within 4Å: Chain A: A.152, D.153, E.156, T.251, S.252 Ligands: MAN.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.153 Water bridges: A:V.142 MAN.14: 6 residues within 4Å: Chain A: V.142, E.156, Q.160, S.252, P.254 Ligands: MAN.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.156, A:Q.160 MAN.15: 3 residues within 4Å: Chain A: V.250, T.253, I.262 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.250 MAN.16: 3 residues within 4Å: Chain A: S.272, F.273, A.274 No protein-ligand interaction detected (PLIP) MAN.17: 1 residues within 4Å: Chain A: T.294 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.295 Water bridges: A:T.294

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

EDO.18: 7 residues within 4Å: Chain A: L.71, N.75, I.180, A.268, V.269, L.271 Ligands: ACT.19 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.75, A:V.269

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

ACT.19: 8 residues within 4Å: Chain A: L.71, A.72, N.75, F.104, I.180, V.183, A.268 Ligands: EDO.18 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.180, A:A.268 Hydrogen bonds: A:N.75 Water bridges: A:A.72

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kuhnel, K. et al., Structure and Quantum Chemical Characterization of Chloroperoxidase Compound 0, a Common Reaction Intermediate of Diverse Heme Enzymes. Proc.Natl.Acad.Sci.USA (2007)

Release Date

2006-12-06

Peptides

CHLOROPEROXIDASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

CHLOROPEROXIDASE

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