SMTL ID : 5gyr.1 (1 other biounit)

Tetrameric Allochromatium vinosum cytochrome c

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

4 x HEC: HEME C(Non-covalent)

HEC.1: 17 residues within 4Å: Chain A: D.83, F.91, V.117, C.121, C.124, H.125, R.129 Chain D: R.12, Q.13, Y.16, M.19, G.20, M.23, Y.58, T.71, R.72, V.73 14 PLIP interactions: 8 interactions with chain D, 6 interactions with chain A, Hydrophobic interactions: D:Y.16, D:Y.16, D:V.73, A:F.91, A:F.91, A:V.117, A:R.129 Hydrogen bonds: D:Q.13, D:R.72, D:V.73 Salt bridges: D:R.12 pi-Stacking: D:Y.16 pi-Cation interactions: A:R.129 Metal complexes: A:H.125 HEC.2: 16 residues within 4Å: Chain B: R.12, Q.13, Y.16, G.20, M.23, Y.58, T.71, R.72, V.73, F.91, V.117, C.121, C.124, H.125, Y.128, R.129 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:Y.16, B:Y.16, B:Y.16, B:V.73, B:F.91, B:F.91, B:V.117, B:R.129 Hydrogen bonds: B:Q.13, B:R.72, B:V.73 Water bridges: B:R.72, B:R.72 Salt bridges: B:R.12 pi-Stacking: B:Y.16 pi-Cation interactions: B:R.129 Metal complexes: B:H.125 HEC.3: 17 residues within 4Å: Chain C: I.9, R.12, Q.13, Y.16, E.17, G.20, M.23, Y.58, T.71, R.72, F.91, V.117, C.121, C.124, H.125, Y.128, R.129 16 PLIP interactions: 15 interactions with chain C, 1 interactions with chain D, Hydrophobic interactions: C:Y.16, C:Y.16, C:Y.16, C:F.91, C:F.91, C:V.117, C:R.129 Hydrogen bonds: C:Q.13, C:T.71, C:R.72, C:V.73 Salt bridges: C:R.12 pi-Stacking: C:Y.16 pi-Cation interactions: C:R.129 Metal complexes: C:H.125 Water bridges: D:E.10 HEC.4: 18 residues within 4Å: Chain A: I.9, R.12, Q.13, Y.16, G.20, M.23, Y.58, T.71, R.72, V.73 Chain D: D.83, F.91, V.117, C.121, C.124, H.125, Y.128, R.129 15 PLIP interactions: 6 interactions with chain D, 9 interactions with chain A, Hydrophobic interactions: D:F.91, D:F.91, D:V.117, D:R.129, A:Y.16, A:Y.16, A:V.73 pi-Cation interactions: D:R.129 Metal complexes: D:H.125 Hydrogen bonds: A:Q.13, A:T.71, A:R.72, A:V.73 Salt bridges: A:R.12 pi-Stacking: A:Y.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamanaka, M. et al., Formation and carbon monoxide-dependent dissociation of Allochromatium vinosum cytochrome c' oligomers using domain-swapped dimers. Protein Sci. (2017)

Release Date

2017-02-08

Peptides

Cytochrome c': ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
M

D
N

Cytochrome c'

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