SMTL ID : 2xil.1

The structure of cytochrome c peroxidase Compound I

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

monomer

Ligands

3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 4 residues within 4Å: Chain A: D.254, D.256, K.257, K.260 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.256, A:K.257 Hydrogen bonds: A:D.256 MPD.3: 4 residues within 4Å: Chain A: E.188, G.189, D.224, G.228 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.224, A:D.224 MPD.6: 5 residues within 4Å: Chain A: P.80, N.184, S.185, G.186 Ligands: MRD.2 No protein-ligand interaction detected (PLIP)

3 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.2: 5 residues within 4Å: Chain A: D.148, S.185, Y.187, N.220 Ligands: MPD.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.187 Hydrogen bonds: A:D.148, A:Y.187, A:Y.187 Water bridges: A:A.147, A:A.147 MRD.4: 3 residues within 4Å: Chain A: K.97, E.98, P.100 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.100 Water bridges: A:E.98 MRD.5: 3 residues within 4Å: Chain A: K.264, K.268, E.271 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.268 Hydrogen bonds: A:K.268 Water bridges: A:K.264, A:E.267

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

HEM.7: 22 residues within 4Å: Chain A: P.44, V.45, R.48, W.51, P.145, D.146, A.147, F.158, L.171, M.172, A.174, H.175, L.177, G.178, K.179, T.180, H.181, N.184, S.185, W.191, L.232, T.234 23 PLIP interactions: 22 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:W.51, A:W.51, A:W.51, A:P.145, A:A.147, A:F.158, A:L.171, A:A.174, A:T.180, A:W.191, A:L.232 Hydrogen bonds: A:K.179, A:H.181, A:N.184, A:S.185 Water bridges: A:Y.36, A:H.181 Salt bridges: A:H.181, A:H.181 pi-Stacking: A:W.51 pi-Cation interactions: A:R.48 Metal complexes: A:H.175, H2O.27

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.8: 2 residues within 4Å: Chain A: Y.36, D.37 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Y.36, A:D.37 Water bridges: A:D.37, A:N.87, A:N.87, A:N.87, A:N.87, A:N.184, A:N.184 Salt bridges: A:H.181

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gumiero, A. et al., Nature of the ferryl heme in compounds I and II. J. Biol. Chem. (2011)

Release Date

2010-07-14

Peptides

CYTOCHROME C PEROXIDASE, MITOCHONDRIAL: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

CYTOCHROME C PEROXIDASE, MITOCHONDRIAL