SMTL ID : 3nbt.2 (1 other biounit)

Crystal structure of trimeric cytochrome c from horse heart

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-trimer

Ligands

3 x HEC: HEME C(Covalent)

HEC.1: 26 residues within 4Å: Chain A: K.13, C.14, C.17, H.18, T.28, G.29, P.30, L.35, R.38, T.40, G.41, Y.48, T.49, N.52, W.59, L.64, Y.67, L.68, T.78, K.79, M.80 Chain B: F.82, I.85, L.94, L.98 Ligands: PEG.3 26 PLIP interactions: 19 interactions with chain A, 6 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: A:T.28, A:P.30, A:L.35, A:W.59, A:L.64, A:Y.67, A:L.68, B:F.82, B:F.82, B:F.82, B:I.85, B:L.94, B:L.98 Hydrogen bonds: A:G.41, A:Y.48, A:T.49, A:N.52, A:N.52, A:T.78, A:T.78, A:K.79 Water bridges: A:Q.42, A:A.43 Salt bridges: A:R.38 Metal complexes: A:H.18, H2O.1 HEC.4: 23 residues within 4Å: Chain B: K.13, C.14, C.17, H.18, T.28, G.29, P.30, L.35, T.40, G.41, Y.48, T.49, N.52, W.59, L.64, Y.67, L.68, T.78, K.79, M.80 Chain C: F.82, L.94 Ligands: PEG.6 24 PLIP interactions: 19 interactions with chain B, 4 interactions with chain C, 1 Ligand-Water interactions, Hydrophobic interactions: B:P.30, B:L.35, B:W.59, B:L.64, B:Y.67, B:L.68, C:F.82, C:F.82, C:F.82, C:L.94 Hydrogen bonds: B:G.41, B:Q.42, B:Y.48, B:T.49, B:N.52, B:T.78, B:T.78, B:K.79 Water bridges: B:R.38, B:R.38, B:R.38 pi-Cation interactions: B:H.18 Metal complexes: B:H.18, H2O.3 HEC.7: 25 residues within 4Å: Chain A: F.82, I.85, L.94, L.98 Chain C: K.13, C.14, C.17, H.18, T.28, G.29, P.30, L.35, T.40, G.41, Y.48, T.49, N.52, W.59, L.64, Y.67, L.68, T.78, K.79, M.80 Ligands: PGE.9 26 PLIP interactions: 19 interactions with chain C, 6 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: C:P.30, C:L.35, C:Y.48, C:W.59, C:L.64, C:Y.67, C:L.68, A:F.82, A:F.82, A:F.82, A:I.85, A:L.94, A:L.98 Hydrogen bonds: C:G.41, C:Q.42, C:Y.48, C:T.49, C:N.52, C:N.52, C:T.78, C:T.78, C:K.79 Water bridges: C:R.38, C:R.38 Metal complexes: C:H.18, H2O.5

3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.2: 6 residues within 4Å: Chain A: K.55, I.57, E.66, K.73, Y.74, P.76 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.55 PG4.5: 6 residues within 4Å: Chain B: K.55, I.57, E.66, K.73, Y.74, P.76 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.55 PG4.8: 6 residues within 4Å: Chain C: K.55, I.57, E.66, K.73, Y.74, P.76 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.55

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 8 residues within 4Å: Chain A: T.47, Y.48, T.49, K.79, I.81, F.82, G.84 Ligands: HEC.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.81 Water bridges: A:A.83, A:G.84 PEG.6: 8 residues within 4Å: Chain B: T.28, T.47, Y.48, T.49, K.79, I.81, G.84 Ligands: HEC.4 2 PLIP interactions: 2 interactions with chain B Water bridges: B:A.83, B:G.84

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.9: 10 residues within 4Å: Chain C: T.28, T.47, Y.48, T.49, K.79, I.81, F.82, A.83, G.84 Ligands: HEC.7 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:A.83 Water bridges: C:A.83, C:A.83

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hirota, S. et al., Cytochrome c polymerization by successive domain swapping at the C-terminal helix. Proc.Natl.Acad.Sci.USA (2010)

Release Date

2010-07-14

Peptides

Cytochrome c: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
D

Cytochrome c

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