SMTL ID : 5kke.1

Crystal Structure of a Domain-swapped Dimer of Yeast Iso-1-cytochrome c with CYMAL5

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x HEC: HEME C(Covalent)

HEC.1: 26 residues within 4Å: Chain A: R.18, C.19, Q.21, C.22, H.23, V.33, G.34, P.35, L.37, I.40, S.45, G.46, Y.51, Y.53, T.54, A.56, W.64, M.69, Y.72, L.73, I.80 Chain B: A.86, F.87, G.88, L.99 Ligands: CM5.4 19 PLIP interactions: 16 interactions with chain A, 2 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: A:Q.21, A:P.35, A:L.37, A:I.40, A:W.64, A:L.73, A:I.80, B:F.87, B:L.99 Hydrogen bonds: A:G.46, A:Y.53, A:T.54, A:W.64 Water bridges: A:Q.47, A:A.48, A:Y.51 pi-Stacking: A:Y.72 Metal complexes: A:H.23, H2O.2 HEC.8: 26 residues within 4Å: Chain A: A.86, F.87, G.88, L.99 Chain B: R.18, C.19, Q.21, C.22, H.23, V.33, G.34, P.35, L.37, I.40, S.45, G.46, Y.51, Y.53, T.54, A.56, W.64, M.69, Y.72, L.73, I.80 Ligands: CM5.11 17 PLIP interactions: 14 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: B:Q.21, B:P.35, B:L.37, B:I.40, B:W.64, B:L.73, B:I.80, A:F.87, A:L.99 Hydrogen bonds: B:G.46, B:T.54, B:W.64 Water bridges: B:Q.47, B:A.48 pi-Stacking: B:Y.72 Metal complexes: B:H.23, H2O.5

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

SO4.2: 3 residues within 4Å: Chain A: S.52, Y.53, N.57 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.52, A:Y.53, A:N.57 Water bridges: A:S.52 SO4.3: 6 residues within 4Å: Chain A: P.81, G.82, T.83, K.84, M.85, K.91 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.82, A:K.84, A:M.85 Water bridges: A:T.83, A:T.83 Salt bridges: A:K.84, A:K.91 SO4.9: 3 residues within 4Å: Chain B: S.52, Y.53, N.57 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.52, B:Y.53, B:N.57 Water bridges: B:S.52 SO4.10: 6 residues within 4Å: Chain B: P.81, G.82, T.83, K.84, M.85, K.91 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.82, B:K.84, B:M.85 Water bridges: B:T.83, B:T.83 Salt bridges: B:K.84, B:K.91

2 x CM5: 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE(Non-covalent)

CM5.4: 10 residues within 4Å: Chain A: S.45, G.46, Y.53, N.57, K.60, V.62, Y.72, K.78, Y.79 Ligands: HEC.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.53, A:N.57, A:K.60, A:K.60, A:Y.72, A:Y.72, A:Y.79, A:Y.79, A:Y.79 Hydrogen bonds: A:K.60 Salt bridges: A:K.60 CM5.11: 10 residues within 4Å: Chain B: S.45, G.46, Y.53, N.57, K.60, V.62, Y.72, K.78, Y.79 Ligands: HEC.8 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.53, B:N.57, B:K.60, B:K.60, B:Y.72, B:Y.72, B:Y.79, B:Y.79, B:Y.79 Hydrogen bonds: B:K.60, B:Y.79 Salt bridges: B:K.60

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 1 residues within 4Å: Chain A: E.93 Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain B: E.93 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: G.28, G.29, H.31, N.36 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.28, A:H.31, A:N.36 GOL.7: 1 residues within 4Å: Chain B: F.87 No protein-ligand interaction detected (PLIP) GOL.13: 4 residues within 4Å: Chain B: G.28, G.29, H.31, N.36 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.28, B:H.31, B:N.36 GOL.14: 1 residues within 4Å: Chain A: F.87 No protein-ligand interaction detected (PLIP)

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
A

B
A

Cytochrome c iso-1

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