SMTL ID : 5klu.1

Crystal Structure of a Domain-swapped Dimer of Yeast Iso-1-cytochrome c with omega-undecylenyl-beta-D-maltopyranoside

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-dimer

Ligands

2 x HEC: HEME C(Covalent)

HEC.1: 25 residues within 4Å: Chain A: R.16, C.17, Q.19, C.20, H.21, V.31, G.32, P.33, L.35, I.38, S.43, G.44, Y.49, Y.51, T.52, A.54, W.62, M.67, Y.70, L.71 Chain B: A.84, F.85, G.86, L.97 Ligands: 6UZ.2 22 PLIP interactions: 18 interactions with chain A, 3 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: A:Q.19, A:P.33, A:L.35, A:L.35, A:I.38, A:I.38, A:W.62, A:L.71, B:F.85, B:L.97, B:L.97 Hydrogen bonds: A:G.44, A:Y.51, A:T.52 Water bridges: A:Q.45, A:A.46, A:Y.49, A:T.52, A:T.52 pi-Stacking: A:Y.70 Metal complexes: A:H.21, H2O.1 HEC.6: 23 residues within 4Å: Chain A: A.84, F.85, G.86, L.88 Chain B: R.16, C.17, Q.19, C.20, H.21, V.31, G.32, P.33, L.35, I.38, S.43, G.44, Y.49, Y.51, T.52, W.62, Y.70, L.71 Ligands: 6UZ.7 13 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: B:L.35, B:I.38, B:I.38, B:W.62, A:F.85, A:L.88 Hydrogen bonds: B:G.44, B:Q.45, B:T.52, B:W.62 pi-Stacking: B:Y.70 Metal complexes: B:H.21, H2O.2

2 x 6UZ: omega-undecylenyl-beta-D-maltopyranoside(Non-covalent)

6UZ.2: 11 residues within 4Å: Chain A: G.44, Y.51, N.55, K.58, V.60, N.65, N.66, E.69, Y.70, Y.77 Ligands: HEC.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.51, A:E.69, A:Y.70, A:Y.70, A:Y.77 Hydrogen bonds: A:N.65, A:N.66 6UZ.7: 7 residues within 4Å: Chain B: Y.51, K.58, W.62, N.66, E.69, Y.77 Ligands: HEC.6 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.51, B:K.58, B:W.62, B:E.69 Hydrogen bonds: B:Y.77, B:Y.77 Salt bridges: B:K.58

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

SO4.3: 4 residues within 4Å: Chain A: G.4, S.5, A.6, K.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.4, A:A.6, A:K.7 Water bridges: A:S.5 Salt bridges: A:K.7 SO4.4: 3 residues within 4Å: Chain A: A.46, E.47, G.48 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.48 SO4.5: 6 residues within 4Å: Chain A: P.79, G.80, T.81, K.82, M.83, K.89 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.80, A:K.82, A:M.83 Salt bridges: A:K.82, A:K.89 SO4.8: 3 residues within 4Å: Chain B: K.89, K.90, E.91 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.89, B:E.91 Water bridges: B:K.92

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
B

Cytochrome c iso-1