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

Crystal structure of dimeric cytochrome c from horse heart

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x HEC: HEME C(Covalent)

HEC.1: 22 residues within 4Å: Chain A: K.13, C.14, C.17, H.18, T.28, G.29, 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: M.80, F.82, L.94 18 PLIP interactions: 3 interactions with chain B, 14 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: B:F.82, B:F.82, B:L.94, A:W.59, A:L.64, A:Y.67, A:L.68 Hydrogen bonds: A:G.41, A:T.49, A:N.52, A:T.78, A:K.79 Water bridges: A:Q.42, A:A.43, A:T.78 Salt bridges: A:R.38 Metal complexes: A:H.18, H2O.1 HEC.4: 22 residues within 4Å: Chain A: F.82, I.85, L.94 Chain B: K.13, C.14, C.17, H.18, T.28, G.29, L.35, T.40, G.41, F.46, Y.48, T.49, N.52, W.59, Y.67, L.68, T.78, M.80 Ligands: PEG.6 19 PLIP interactions: 14 interactions with chain B, 4 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: B:L.35, B:F.46, B:W.59, B:Y.67, B:L.68, A:F.82, A:F.82, A:F.82, A:I.85 Hydrogen bonds: B:G.41, B:Y.48, B:T.49, B:N.52, B:N.52, B:T.78 Water bridges: B:Q.42, B:A.43 Metal complexes: B:H.18, H2O.4

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 5 residues within 4Å: Chain A: Y.97, K.100, A.101, E.104 Chain B: K.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.97, A:E.104 Salt bridges: A:K.100 PO4.5: 5 residues within 4Å: Chain A: K.7 Chain B: Y.97, K.100, A.101, E.104 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.97, B:E.104 Water bridges: B:E.104, B:E.104 Salt bridges: B:K.100

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

PG4.3: 5 residues within 4Å: Chain A: K.55, E.66, K.73, Y.74, P.76 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.55

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

PEG.6: 6 residues within 4Å: Chain A: Q.16, C.17, T.28 Chain B: Q.16, T.28 Ligands: HEC.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.28 Water bridges: B:T.28

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Cytochrome c

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