SMTL ID : 4mu8.2 (1 other biounit)

Crystal structure of an oxidized form of yeast iso-1-cytochrome c at pH 8.8

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: S.7, A.8, K.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.8, A:K.9 Water bridges: A:G.6 SO4.3: 2 residues within 4Å: Chain A: K.84, M.85 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.85 Water bridges: A:A.86 SO4.4: 3 residues within 4Å: Chain A: T.54, D.55, A.56 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.55, A:D.55 Water bridges: A:D.55, A:A.56 SO4.5: 4 residues within 4Å: Chain A: K.91, K.92, E.93, K.94 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.91, A:E.93 Water bridges: A:K.94, A:R.96

1 x HEC: HEME C(Non-covalent)

HEC.2: 29 residues within 4Å: Chain A: F.15, R.18, C.19, C.22, H.23, V.33, G.34, P.35, L.37, I.40, S.45, G.46, Q.47, A.48, Y.51, Y.53, T.54, N.57, W.64, M.69, Y.72, L.73, T.83, K.84, M.85, F.87, L.90, L.99, L.103 26 PLIP interactions: 25 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:L.37, A:L.37, A:I.40, A:W.64, A:L.73, A:K.84, A:F.87, A:F.87, A:F.87, A:L.90, A:L.99 Hydrogen bonds: A:G.46, A:Y.53, A:T.54, A:T.54, A:N.57, A:W.64, A:T.83, A:T.83, A:K.84 Water bridges: A:Q.47, A:A.48 Salt bridges: A:K.84 pi-Stacking: A:Y.72 Metal complexes: A:H.23, H2O.1

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: K.60, V.62, N.68, E.71, Y.79 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.71, A:Y.79 Water bridges: A:K.60

2 x TBU: TERTIARY-BUTYL ALCOHOL(Non-functional Binders)

TBU.7: 3 residues within 4Å: Chain A: Q.21, C.22, V.33 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.21 TBU.8: 4 residues within 4Å: Chain A: A.56, K.59, K.60, P.81 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.56, A:K.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McClelland, L.J. et al., Structure of a mitochondrial cytochrome c conformer competent for peroxidase activity. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2014-06-04

Peptides

Cytochrome c iso-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Cytochrome c iso-1

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