SMTL ID : 5t7h.2 (1 other biounit)

Crystal structure of dimeric yeast iso-1-cytochrome C with CYMAL6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: S.8, A.9, K.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.8, A:A.9, A:K.10 SO4.2: 3 residues within 4Å: Chain A: S.53, Y.54, N.58 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.54, A:Y.54, A:N.58 Water bridges: A:S.53 SO4.3: 7 residues within 4Å: Chain A: I.81, P.82, G.83, T.84, K.85, M.86, K.92 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.83, A:T.84, A:K.85, A:M.86 Water bridges: A:G.90, A:K.92 Salt bridges: A:K.85, A:K.92 SO4.6: 3 residues within 4Å: Chain B: S.53, Y.54, N.58 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.54, B:N.58, B:N.58 Water bridges: B:Y.52, B:S.53 SO4.7: 6 residues within 4Å: Chain B: P.82, G.83, T.84, K.85, M.86, K.92 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.83, B:K.85, B:M.86 Water bridges: B:T.84 Salt bridges: B:K.85, B:K.92

2 x ZE7: 6-cyclohexylhexan-1-ol(Non-covalent)

ZE7.4: 7 residues within 4Å: Chain A: S.46, G.47, K.61, W.65, Y.73, Y.80 Ligands: HEC.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:K.61, A:W.65, A:Y.73, A:Y.80, A:Y.80 Hydrogen bonds: A:Y.80 ZE7.8: 9 residues within 4Å: Chain B: S.46, Y.54, N.58, K.61, W.65, N.69, Y.73, Y.80 Ligands: HEC.9 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.54, B:N.58, B:K.61, B:W.65, B:Y.73, B:Y.73, B:Y.80, B:Y.80

2 x HEC: HEME C(Covalent)

HEC.5: 25 residues within 4Å: Chain A: R.19, C.20, Q.22, C.23, H.24, V.34, G.35, P.36, L.38, I.41, S.46, G.47, Y.52, Y.54, T.55, A.57, W.65, M.70, Y.73, L.74 Chain B: A.87, F.88, G.89, L.100 Ligands: ZE7.4 17 PLIP interactions: 13 interactions with chain A, 3 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: A:Q.22, A:P.36, A:I.41, A:W.65, A:L.74, B:F.88, B:L.100, B:L.100 Hydrogen bonds: A:G.47, A:Y.54, A:T.55 Water bridges: A:Q.48, A:Q.48, A:Y.52 pi-Stacking: A:Y.73 Metal complexes: A:H.24, H2O.2 HEC.9: 24 residues within 4Å: Chain A: A.87, F.88, G.89, L.100 Chain B: R.19, C.20, Q.22, C.23, H.24, V.34, G.35, P.36, L.38, S.46, G.47, Y.52, Y.54, T.55, A.57, W.65, M.70, Y.73, L.74 Ligands: ZE7.8 17 PLIP interactions: 14 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: B:Q.22, B:P.36, B:L.38, B:W.65, B:L.74, A:F.88, A:L.100 Hydrogen bonds: B:G.47, B:T.55, B:W.65 Water bridges: B:R.44, B:Q.48, B:A.49, B:T.55 pi-Stacking: B:Y.73 Metal complexes: B:H.24, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McClelland, L.J. et al., Cytochrome c Can Form a Well-Defined Binding Pocket for Hydrocarbons. J. Am. Chem. Soc. (2016)

Release Date

2017-03-22

Peptides

Cytochrome c iso-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

Cytochrome c iso-1

Related Entries With Identical Sequence