SMTL ID : 2yk3.1

CRITHIDIA FASCICULATA CYTOCHROME C

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-hexamer

Ligands

6 x HEC: HEME C(Covalent)

HEC.1: 30 residues within 4Å: Chain A: R.24, A.25, Q.27, C.28, H.29, V.39, G.40, P.41, L.43, L.46, S.51, G.52, I.54, Y.57, Y.59, S.60, N.63, W.70, L.75, Y.78, L.79, T.89, K.90, M.91, S.92, F.93, V.105, L.109 Chain B: N.37, G.38 28 PLIP interactions: 27 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:A.25, A:V.39, A:L.43, A:L.46, A:Y.57, A:W.70, A:L.75, A:L.79, A:K.90, A:M.91, A:F.93, A:F.93, A:F.93, A:V.105, A:L.109, B:N.37 Hydrogen bonds: A:G.52, A:T.53, A:S.60, A:N.63, A:T.89, A:K.90 Water bridges: A:I.54, A:I.54, A:T.89 Salt bridges: A:K.90 pi-Stacking: A:Y.78 Metal complexes: A:H.29 HEC.5: 30 residues within 4Å: Chain B: R.24, A.25, Q.27, C.28, H.29, V.39, G.40, P.41, L.43, L.46, S.51, G.52, I.54, Y.57, Y.59, S.60, N.63, W.70, L.75, Y.78, L.79, T.89, K.90, M.91, S.92, F.93, M.96, V.105 Chain C: N.37, G.38 28 PLIP interactions: 27 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:A.25, B:V.39, B:L.43, B:L.46, B:Y.57, B:W.70, B:L.75, B:Y.78, B:L.79, B:K.90, B:M.91, B:F.93, B:F.93, B:F.93, B:V.105, C:N.37 Hydrogen bonds: B:G.52, B:Y.59, B:S.60, B:N.63, B:N.63, B:K.90 Water bridges: B:T.53, B:I.54, B:T.89 Salt bridges: B:K.90 pi-Stacking: B:Y.78 Metal complexes: B:H.29 HEC.8: 31 residues within 4Å: Chain A: N.37, G.38 Chain C: R.24, A.25, Q.27, C.28, H.29, V.39, G.40, P.41, L.43, L.46, S.51, G.52, I.54, Y.57, Y.59, S.60, N.63, W.70, L.75, Y.78, L.79, T.89, K.90, M.91, S.92, F.93, M.96, V.105, L.109 27 PLIP interactions: 26 interactions with chain C, 1 interactions with chain A, Hydrophobic interactions: C:A.25, C:V.39, C:L.43, C:L.46, C:Y.57, C:W.70, C:L.75, C:Y.78, C:L.79, C:K.90, C:M.91, C:F.93, C:F.93, C:F.93, C:L.109, A:N.37 Hydrogen bonds: C:G.52, C:T.53, C:Y.59, C:S.60, C:N.63, C:K.90 Water bridges: C:I.54, C:I.54 Salt bridges: C:K.90 pi-Stacking: C:Y.78 Metal complexes: C:H.29 HEC.11: 30 residues within 4Å: Chain D: R.24, A.25, Q.27, C.28, H.29, V.39, G.40, P.41, L.43, L.46, S.51, G.52, I.54, Y.57, Y.59, S.60, N.63, W.70, L.75, Y.78, L.79, T.89, K.90, M.91, S.92, F.93, V.105, L.109 Chain E: N.37, G.38 29 PLIP interactions: 28 interactions with chain D, 1 interactions with chain E, Hydrophobic interactions: D:A.25, D:V.39, D:L.43, D:L.46, D:Y.57, D:W.70, D:L.75, D:L.79, D:K.90, D:M.91, D:F.93, D:F.93, D:F.93, D:V.105, D:L.109, E:N.37 Hydrogen bonds: D:G.52, D:T.53, D:Y.59, D:S.60, D:N.63, D:T.89, D:T.89, D:K.90 Water bridges: D:I.54, D:I.54 Salt bridges: D:K.90 pi-Stacking: D:Y.78 Metal complexes: D:H.29 HEC.15: 30 residues within 4Å: Chain E: R.24, A.25, Q.27, C.28, H.29, V.39, G.40, P.41, L.43, L.46, S.51, G.52, I.54, Y.57, Y.59, S.60, N.63, W.70, L.75, Y.78, L.79, T.89, K.90, M.91, S.92, F.93, M.96, V.105 Chain F: N.37, G.38 27 PLIP interactions: 26 interactions with chain E, 1 interactions with chain F, Hydrophobic interactions: E:A.25, E:V.39, E:L.43, E:L.46, E:Y.57, E:W.70, E:L.75, E:Y.78, E:L.79, E:K.90, E:M.91, E:F.93, E:F.93, E:F.93, E:V.105, F:N.37 Hydrogen bonds: E:G.52, E:S.60, E:N.63, E:N.63, E:T.89, E:K.90 Water bridges: E:T.53, E:I.54 Salt bridges: E:K.90 pi-Stacking: E:Y.78 Metal complexes: E:H.29 HEC.18: 31 residues within 4Å: Chain D: N.37, G.38 Chain F: R.24, A.25, Q.27, C.28, H.29, V.39, G.40, P.41, L.43, L.46, S.51, G.52, I.54, Y.57, Y.59, S.60, N.63, W.70, L.75, Y.78, L.79, T.89, K.90, M.91, S.92, F.93, M.96, V.105, L.109 27 PLIP interactions: 26 interactions with chain F, 1 interactions with chain D, Hydrophobic interactions: F:A.25, F:V.39, F:L.43, F:L.46, F:Y.57, F:W.70, F:L.75, F:Y.78, F:L.79, F:K.90, F:M.91, F:F.93, F:F.93, F:F.93, F:L.109, D:N.37 Hydrogen bonds: F:G.52, F:T.53, F:S.60, F:N.63, F:T.89, F:K.90 Water bridges: F:I.54, F:I.54 Salt bridges: F:K.90 pi-Stacking: F:Y.78 Metal complexes: F:H.29

14 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: R.24, G.95, M.96, K.97 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.95, A:K.97 Water bridges: A:R.24, A:K.98, A:E.101, A:E.101, A:E.101 Salt bridges: A:R.24 SO4.3: 1 residues within 4Å: Chain A: R.49 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.55 Salt bridges: A:R.49 SO4.4: 3 residues within 4Å: Chain A: K.90 Chain B: K.90 Chain C: K.90 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B, 2 interactions with chain A Salt bridges: C:K.90, B:K.90, A:K.90 Water bridges: B:K.90, A:K.90 SO4.6: 4 residues within 4Å: Chain B: R.24, G.95, M.96, K.97 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.97 Water bridges: B:R.24, B:R.24, B:K.98, B:E.101, B:E.101 Salt bridges: B:R.24 SO4.7: 1 residues within 4Å: Chain B: R.49 3 PLIP interactions: 3 interactions with chain B Water bridges: B:E.55, B:E.55 Salt bridges: B:R.49 SO4.9: 5 residues within 4Å: Chain C: R.24, G.95, M.96, K.97, K.98 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:K.97 Water bridges: C:R.24, C:K.98, C:E.101, C:E.101 Salt bridges: C:R.24 SO4.10: 2 residues within 4Å: Chain C: R.49, T.53 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.53 Water bridges: C:R.49, C:R.49, C:E.55 Salt bridges: C:R.49 SO4.12: 4 residues within 4Å: Chain D: R.24, G.95, M.96, K.97 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:G.95, D:K.97 Water bridges: D:R.24, D:K.98, D:K.98, D:E.101, D:E.101 Salt bridges: D:R.24 SO4.13: 1 residues within 4Å: Chain D: R.49 2 PLIP interactions: 2 interactions with chain D Water bridges: D:E.55 Salt bridges: D:R.49 SO4.14: 3 residues within 4Å: Chain D: K.90 Chain E: K.90 Chain F: K.90 5 PLIP interactions: 2 interactions with chain E, 2 interactions with chain D, 1 interactions with chain F Water bridges: E:K.90, D:K.90 Salt bridges: E:K.90, D:K.90, F:K.90 SO4.16: 4 residues within 4Å: Chain E: R.24, G.95, M.96, K.97 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:K.97 Water bridges: E:R.24, E:R.24, E:K.98, E:K.98, E:E.101 Salt bridges: E:R.24 SO4.17: 1 residues within 4Å: Chain E: R.49 2 PLIP interactions: 2 interactions with chain E Water bridges: E:E.55 Salt bridges: E:R.49 SO4.19: 5 residues within 4Å: Chain F: R.24, G.95, M.96, K.97, K.98 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:K.97 Water bridges: F:R.24, F:R.24, F:E.101, F:E.101 Salt bridges: F:R.24 SO4.20: 2 residues within 4Å: Chain F: R.49, T.53 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:T.53 Water bridges: F:R.49, F:R.49, F:E.55 Salt bridges: F:R.49

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fulop, V. et al., Structure of a Trypanosomatid Mitochondrial Cytochrome C with Heme Attached Via Only One Thioether Bond and Implications for the Substrate Recognition Requirements of Heme Lyase. FEBS J. (2009)

Release Date

2011-06-15

Peptides

CYTOCHROME C: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

CYTOCHROME C