SMTL ID : 3wui.1

Dimeric horse cytochrome c formed by refolding from molten globule state

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.35, T.40, G.41, 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, PEG.5, PEG.10 23 PLIP interactions: 4 interactions with chain B, 18 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: B:I.81, B:A.83, B:I.85, B:L.98, A:P.30, A:L.35, A:F.46, A:W.59, A:L.64, A:Y.67, A:L.68 Hydrogen bonds: A:G.41, A:Q.42, A:T.49, A:N.52, A:N.52, A:T.78, A:T.78, A:K.79 Water bridges: A:R.38, A:A.43 Metal complexes: A:H.18, H2O.1 HEC.6: 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.35, T.40, G.41, F.46, Y.48, T.49, N.52, W.59, L.64, Y.67, L.68, T.78, K.79, M.80 Ligands: PEG.5, PEG.9, PEG.10 23 PLIP interactions: 18 interactions with chain B, 4 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: B:P.30, B:L.35, B:F.46, B:W.59, B:L.64, B:Y.67, B:L.68, A:I.81, A:A.83, A:I.85, A:L.98 Hydrogen bonds: B:G.41, B:Q.42, B:Y.48, B:T.49, B:N.52, B:N.52, B:T.78, B:K.79 Water bridges: B:R.38, B:A.43 Metal complexes: B:H.18, H2O.4

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

PG4.2: 5 residues within 4Å: Chain A: K.55, E.66, K.73, Y.74, P.76 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.55, A:K.55 PG4.7: 5 residues within 4Å: Chain B: K.55, E.66, K.73, Y.74, P.76 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.55, B:K.55

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

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

4 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.48, A:T.49 PEG.5: 8 residues within 4Å: Chain A: Q.16, C.17, I.81 Chain B: Q.16, T.28 Ligands: HEC.1, HEC.6, PEG.10 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.16, B:T.28, A:Q.16 PEG.9: 5 residues within 4Å: Chain B: T.47, Y.48, T.49, K.79 Ligands: HEC.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.48, B:T.49 PEG.10: 8 residues within 4Å: Chain A: Q.16, T.28 Chain B: Q.16, C.17, I.81 Ligands: HEC.1, PEG.5, HEC.6 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.16, B:Q.16 Water bridges: A:T.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deshpande, M.S. et al., Formation of domain-swapped oligomer of cytochrome C from its molten globule state oligomer. Biochemistry (2014)

Release Date

2014-07-16

Peptides

Cytochrome c: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Cytochrome c

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