SMTL ID : 1gyo.1

Crystal structure of the di-tetraheme cytochrome c3 from Desulfovibrio gigas at 1.2 Angstrom resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

homo-dimer

Ligands

8 x HEC: HEME C(Covalent)

HEC.1: 19 residues within 4Å: Chain A: L.1, V.3, P.4, V.7, I.9, M.26, H.28, H.31, V.34, S.35, C.36, C.39, H.40, F.49, K.51, C.52 Chain B: F.43 Ligands: HEC.3, HEC.5 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:L.1, A:V.3, A:V.3, A:V.7, A:I.9, A:H.31, A:V.34, A:F.49, A:F.49, A:F.49, B:F.43 Hydrogen bonds: A:C.52 Water bridges: A:F.49 Salt bridges: A:K.51, A:K.51 pi-Stacking: A:F.49 Metal complexes: A:H.28, A:H.40 HEC.2: 17 residues within 4Å: Chain A: C.39, H.40, H.41, M.42, Q.50, K.51, C.52, C.55, H.56, E.65, R.66, K.70, A.71, S.74, S.76, I.78, S.79 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:Q.50, A:R.66, A:A.71, A:I.78 Hydrogen bonds: A:S.74 Water bridges: A:K.70 Salt bridges: A:K.70 Metal complexes: A:H.41, A:H.56 HEC.3: 23 residues within 4Å: Chain A: I.9, V.24, M.26, S.27, K.30, H.31, V.34, S.38, C.39, W.72, E.77, I.78, S.79, C.80, C.83, H.84, M.87, Q.93, T.94, G.95, P.96 Ligands: HEC.1, HEC.4 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:I.9, A:V.24, A:K.30, A:V.34, A:V.34, A:W.72, A:P.96 Metal complexes: A:H.31, A:H.84 HEC.4: 23 residues within 4Å: Chain A: I.9, T.10, H.18, F.21, G.22, K.23, V.24, R.59, R.62, F.68, Y.69, W.72, H.73, C.80, R.81, H.84, P.96, I.97, G.98, C.99, C.103, H.104 Ligands: HEC.3 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:I.9, A:I.9, A:H.18, A:F.21, A:F.21, A:V.24, A:V.24, A:F.68, A:F.68, A:Y.69, A:W.72, A:W.72 Hydrogen bonds: A:H.18 Water bridges: A:R.59 Salt bridges: A:R.59, A:H.104 pi-Stacking: A:Y.69, A:H.73, A:H.104 Metal complexes: A:H.73, A:H.104 HEC.5: 19 residues within 4Å: Chain A: L.1, F.43 Chain B: D.2, V.3, V.7, I.9, M.26, H.28, H.31, V.34, S.35, C.36, C.39, H.40, F.49, K.51, C.52 Ligands: HEC.1, HEC.7 19 PLIP interactions: 16 interactions with chain B, 3 interactions with chain A, Hydrophobic interactions: B:V.3, B:V.7, B:I.9, B:H.31, B:V.34, B:F.49, B:F.49, B:F.49, A:L.1, A:L.1, A:F.43 Hydrogen bonds: B:C.52 Water bridges: B:V.8, B:K.51, B:A.53 Salt bridges: B:K.51, B:K.51 Metal complexes: B:H.28, B:H.40 HEC.6: 18 residues within 4Å: Chain B: C.39, H.40, H.41, M.42, K.51, C.52, C.55, H.56, E.65, R.66, K.70, A.71, W.72, S.74, S.76, I.78, S.79 Ligands: GOL.9 9 PLIP interactions: 9 interactions with chain B, Hydrophobic interactions: B:R.66, B:A.71, B:W.72, B:I.78 Hydrogen bonds: B:S.74 Salt bridges: B:R.66, B:K.70 Metal complexes: B:H.41, B:H.56 HEC.7: 21 residues within 4Å: Chain B: I.9, V.24, M.26, K.30, H.31, V.34, C.39, W.72, E.77, I.78, S.79, C.80, C.83, H.84, M.87, Q.93, T.94, G.95, P.96 Ligands: HEC.5, HEC.8 10 PLIP interactions: 10 interactions with chain B, Hydrophobic interactions: B:I.9, B:V.24, B:K.30, B:V.34, B:V.34, B:W.72, B:P.96 Salt bridges: B:K.30 Metal complexes: B:H.31, B:H.84 HEC.8: 23 residues within 4Å: Chain B: I.9, T.10, A.11, F.21, G.22, K.23, V.24, R.59, R.62, F.68, Y.69, W.72, H.73, C.80, R.81, H.84, P.96, I.97, G.98, C.99, C.103, H.104 Ligands: HEC.7 23 PLIP interactions: 23 interactions with chain B, Hydrophobic interactions: B:I.9, B:I.9, B:F.21, B:F.21, B:V.24, B:V.24, B:F.68, B:F.68, B:Y.69, B:W.72, B:W.72 Water bridges: B:R.62, B:R.62, B:R.62, B:R.62 Salt bridges: B:R.59, B:R.62, B:H.104 pi-Stacking: B:Y.69, B:H.73, B:H.104 Metal complexes: B:H.73, B:H.104

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 6 residues within 4Å: Chain B: M.42, D.44, D.48, Q.50 Ligands: HEC.6, GOL.10 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.50 Water bridges: B:M.42, B:M.42, B:D.44 GOL.10: 6 residues within 4Å: Chain A: C.5, A.29, R.32 Chain B: D.44, C.46 Ligands: GOL.9 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.32 Water bridges: B:D.44

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Aragao, D. et al., Structure of Dimeric Cytochrome C3 from Desulfovibrio Gigas at 1.2 A Resolution. Acta Crystallogr.,Sect.D (2003)

Release Date

2002-05-24

Peptides

CYTOCHROME C3, A DIMERIC CLASS III C-TYPE CYTOCHROME: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

CYTOCHROME C3, A DIMERIC CLASS III C-TYPE CYTOCHROME