SMTL ID : 3wc8.1

Dimeric horse cytochrome c obtained by refolding with desalting method

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x HEC: HEME C(Covalent)

HEC.1: 29 residues within 4Å: Chain A: K.13, C.14, C.17, H.18, T.28, G.29, P.30, L.32, L.35, T.40, G.41, Q.42, F.46, Y.48, T.49, N.52, W.59, L.64, Y.67, L.68, T.78, K.79, M.80 Chain B: I.81, A.83, I.85, L.94, L.98 Ligands: PEG.4 24 PLIP interactions: 19 interactions with chain A, 4 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: A:T.28, A:P.30, A:L.32, A:L.35, A:F.46, A:W.59, A:L.64, A:Y.67, A:L.68, B:I.81, B:I.85, B:L.94, B:L.98 Hydrogen bonds: A:G.41, A:Q.42, A:Y.48, A:T.49, A:N.52, A:T.78, A:K.79 Water bridges: A:R.38, A:R.38 Metal complexes: A:H.18, H2O.1 HEC.7: 29 residues within 4Å: Chain A: I.81, A.83, I.85, L.94, L.98 Chain B: K.13, C.14, C.17, H.18, T.28, G.29, P.30, L.32, L.35, T.40, G.41, Q.42, F.46, Y.48, T.49, N.52, W.59, L.64, Y.67, L.68, T.78, K.79, M.80 Ligands: PEG.10 24 PLIP interactions: 19 interactions with chain B, 4 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: B:T.28, B:P.30, B:L.32, B:L.35, B:F.46, B:W.59, B:L.64, B:Y.67, B:L.68, A:I.81, A:I.85, A:L.94, A:L.98 Hydrogen bonds: B:G.41, B:Q.42, B:T.49, B:N.52, B:T.78, B:T.78, B:K.79 Water bridges: B:R.38, B:R.38 Metal complexes: B:H.18, H2O.3

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

PO4.2: 5 residues within 4Å: Chain A: K.7 Chain B: Y.97, K.100, A.101, E.104 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.97, B:E.104 Salt bridges: B:K.100, A:K.7 PO4.8: 5 residues within 4Å: Chain A: Y.97, K.100, A.101, E.104 Chain B: K.7 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:K.7, A:K.100 Hydrogen bonds: A:E.104

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

PG4.3: 4 residues within 4Å: Chain A: K.55, K.73, Y.74, P.76 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.55 PG4.9: 4 residues within 4Å: Chain B: K.55, K.73, Y.74, P.76 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.55

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

PEG.4: 5 residues within 4Å: Chain A: T.47, Y.48, T.49, K.79 Ligands: HEC.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.49, A:F.82 Water bridges: A:F.82 PEG.5: 5 residues within 4Å: Chain A: G.24, H.26, N.31, H.33, P.44 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.31 PEG.6: 7 residues within 4Å: Chain A: Q.16, C.17, I.81 Chain B: Q.16, C.17, I.81 Ligands: PEG.12 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.16, A:Q.16 Water bridges: B:Q.16, B:T.28 PEG.10: 5 residues within 4Å: Chain B: T.47, Y.48, T.49, K.79 Ligands: HEC.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.49, B:F.82 Water bridges: B:F.82 PEG.11: 5 residues within 4Å: Chain B: G.24, H.26, N.31, H.33, P.44 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.31 PEG.12: 7 residues within 4Å: Chain A: Q.16, C.17, I.81 Chain B: Q.16, C.17, I.81 Ligands: PEG.6 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Q.16, A:Q.16 Water bridges: B:T.28, A:Q.16, A:T.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Parui, P.P. et al., Formation of Oligomeric Cytochrome c during Folding by Intermolecular Hydrophobic Interaction between N- and C-Terminal alpha-Helices. Biochemistry (2013)

Release Date

2013-12-11

Peptides

Cytochrome c: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Cytochrome c

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