SMTL ID : 6k7c.1

Dimeric Shewanella violacea cytochrome c5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.15 Å

Oligo State

homo-dimer

Ligands

2 x HEC: HEME C(Covalent)

HEC.1: 26 residues within 4Å: Chain A: A.10, C.11, C.14, H.15, A.52 Chain B: A.20, G.21, A.22, P.23, W.31, R.34, Q.37, L.42, T.45, V.46, K.50, A.52, M.53, P.54, G.57, M.58, C.59, Y.67, A.70, I.71, M.74 22 PLIP interactions: 21 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:A.22, B:W.31, B:W.31, B:R.34, B:L.42, B:T.45, B:V.46, B:A.52, B:M.58, B:Y.67, B:A.70, B:I.71, B:I.71 Hydrogen bonds: B:R.34, B:Q.37 Water bridges: B:A.20, B:R.34, B:K.50, B:K.50 Salt bridges: B:K.50, B:K.50 Metal complexes: A:H.15 HEC.3: 28 residues within 4Å: Chain A: A.20, G.21, A.22, P.23, W.31, R.34, Q.37, L.42, T.45, V.46, K.50, G.51, A.52, M.53, P.54, G.57, M.58, C.59, Y.67, A.70, I.71, M.74 Chain B: V.6, A.10, C.11, C.14, H.15, A.52 25 PLIP interactions: 22 interactions with chain A, 3 interactions with chain B, Hydrophobic interactions: A:A.22, A:W.31, A:W.31, A:L.42, A:T.45, A:V.46, A:A.52, A:Y.67, A:A.70, A:I.71, A:I.71, B:V.6 Hydrogen bonds: A:Q.37 Water bridges: A:A.20, A:R.34, A:R.34, A:T.45, A:K.50, A:K.50, A:A.52 Salt bridges: A:R.34, A:K.50, A:K.50 pi-Stacking: B:H.15 Metal complexes: B:H.15

1 x NO3: NITRATE ION(Non-functional Binders)

NO3.2: 5 residues within 4Å: Chain A: E.2, G.3, K.4, A.5, V.6 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.2, A:G.3, A:A.5, A:V.6 Water bridges: A:K.4, A:K.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, H. et al., Protein surface charge effect on 3D domain swapping in cells for c-type cytochromes. Biochim Biophys Acta Proteins Proteom (2019)

Release Date

2019-09-04

Peptides

Soluble cytochrome cA: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Soluble cytochrome cA

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