SMTL ID : 1nml.2 (1 other biounit)

Di-haemic Cytochrome c Peroxidase from Pseudomonas nautica 617, form IN (pH 4.0)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

4 x HEC: HEME C(Covalent)

HEC.1: 27 residues within 4Å: Chain A: F.38, I.49, S.50, C.51, C.54, H.55, T.67, I.69, G.70, H.71, W.73, R.78, N.79, S.80, P.81, V.83, A.86, N.89, Q.92, F.93, P.108, G.112, M.115, I.156, E.160, R.246 Ligands: CIT.4 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:F.38, A:I.49, A:T.67, A:I.69, A:R.78, A:P.81, A:V.83, A:F.93, A:P.108, A:I.156, A:E.160 Hydrogen bonds: A:N.89, A:F.93 Water bridges: A:R.246 Salt bridges: A:H.71, A:R.78, A:R.246 Metal complexes: A:H.55, A:H.71 HEC.2: 26 residues within 4Å: Chain A: F.192, G.196, C.197, C.200, H.201, Y.212, F.214, G.215, L.216, F.245, R.246, A.247, S.248, L.250, I.253, Y.259, F.260, H.261, A.271, V.272, M.275, L.280, T.282, L.284, I.292 Ligands: CIT.3 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:F.192, A:Y.212, A:F.214, A:L.250, A:F.260, A:F.260, A:A.271, A:V.272, A:M.275, A:L.280, A:T.282, A:L.284, A:I.292 Hydrogen bonds: A:L.216, A:S.248, A:F.260, A:H.261 Water bridges: A:T.256 Salt bridges: A:H.261 Metal complexes: A:H.201 HEC.7: 27 residues within 4Å: Chain B: F.38, I.49, S.50, C.51, C.54, H.55, T.67, I.69, G.70, H.71, W.73, R.78, N.79, S.80, P.81, V.83, A.86, N.89, Q.92, F.93, P.108, G.112, M.115, I.156, E.160, R.246 Ligands: CIT.10 20 PLIP interactions: 20 interactions with chain B, Hydrophobic interactions: B:F.38, B:I.49, B:T.67, B:I.69, B:R.78, B:P.81, B:V.83, B:F.93, B:P.108, B:I.156, B:E.160 Hydrogen bonds: B:N.89, B:F.93 Water bridges: B:E.114, B:R.246 Salt bridges: B:H.71, B:R.78, B:R.246 Metal complexes: B:H.55, B:H.71 HEC.8: 26 residues within 4Å: Chain B: F.192, G.196, C.197, C.200, H.201, Y.212, F.214, G.215, L.216, F.245, R.246, A.247, S.248, L.250, I.253, Y.259, F.260, H.261, A.271, V.272, M.275, L.280, T.282, L.284, I.292 Ligands: CIT.9 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:F.192, B:Y.212, B:F.214, B:L.250, B:F.260, B:F.260, B:A.271, B:V.272, B:M.275, B:L.280, B:T.282, B:L.284, B:I.292 Hydrogen bonds: B:L.216, B:S.248, B:F.260, B:H.261 Salt bridges: B:H.261 Metal complexes: B:H.201

8 x CIT: CITRIC ACID(Non-functional Binders)

CIT.3: 12 residues within 4Å: Chain A: N.79, P.81, F.93, W.94, F.245, R.246, A.247, S.248, P.249, F.260, H.261 Ligands: HEC.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.93 Hydrogen bonds: A:W.94, A:R.246, A:R.246, A:F.260 Water bridges: A:R.246 Salt bridges: A:R.246 CIT.4: 10 residues within 4Å: Chain A: L.43, S.44, I.49, S.50, C.51, H.71, M.115, S.116, S.117 Ligands: HEC.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.43 Hydrogen bonds: A:L.43, A:H.71, A:S.116, A:S.117 Water bridges: A:S.45, A:S.45, A:C.51, A:S.116, A:S.116, A:S.117 CIT.5: 6 residues within 4Å: Chain A: S.267, L.268, E.269, K.290, V.293, K.297 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.268, A:E.269, A:K.297 Water bridges: A:K.290 Salt bridges: A:K.297, A:K.297 CIT.6: 2 residues within 4Å: Chain A: E.237, Q.279 No protein-ligand interaction detected (PLIP) CIT.9: 12 residues within 4Å: Chain B: N.79, P.81, F.93, W.94, F.245, R.246, A.247, S.248, P.249, F.260, H.261 Ligands: HEC.8 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.93 Hydrogen bonds: B:W.94, B:R.246, B:R.246, B:F.260 Water bridges: B:R.246 Salt bridges: B:R.246 CIT.10: 10 residues within 4Å: Chain B: L.43, S.44, I.49, S.50, C.51, H.71, M.115, S.116, S.117 Ligands: HEC.7 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.43 Hydrogen bonds: B:L.43, B:H.71, B:S.116, B:S.117 Water bridges: B:S.45, B:S.45, B:C.51, B:S.116, B:S.116, B:S.117 CIT.11: 6 residues within 4Å: Chain B: S.267, L.268, E.269, K.290, V.293, K.297 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:L.268, B:E.269, B:K.297 Water bridges: B:K.290 Salt bridges: B:K.297, B:K.297 CIT.12: 2 residues within 4Å: Chain B: E.237, Q.279 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dias, J.M. et al., Structural basis for the mechanism of Ca(2+) activation of the di-heme cytochrome c peroxidase from Pseudomonas nautica 617. Structure (2004)

Release Date

2004-01-13

Peptides

di-haem cytochrome c peroxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

di-haem cytochrome c peroxidase

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