SMTL ID : 2zbo.7 (6 other biounits)

Crystal structure of low-redox-potential cytochrom c6 from brown alga Hizikia fusiformis at 1.6 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-hexamer

Ligands

6 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.1: 25 residues within 4Å: Chain A: N.13, C.14, C.17, H.18, N.23, I.25, M.26, K.29, T.30, L.31, A.35, L.36, N.39, M.41, I.47, Q.50, V.51, K.55, N.56, A.57, M.58, P.59, F.61, V.77 Chain B: A.12 19 PLIP interactions: 18 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:N.13, A:I.25, A:I.25, A:L.31, A:I.47, A:V.51, A:F.61, A:V.77, B:A.12 Hydrogen bonds: A:T.30, A:N.39, A:N.56 Water bridges: A:K.29, A:K.29, A:K.29, A:K.29, A:Q.50 Salt bridges: A:K.29 Metal complexes: A:H.18 HEM.3: 25 residues within 4Å: Chain B: N.13, C.14, C.17, H.18, N.23, I.25, M.26, K.29, T.30, L.31, A.35, L.36, N.39, M.41, I.47, Q.50, V.51, K.55, N.56, A.57, M.58, P.59, F.61, V.77 Chain C: A.12 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:N.13, B:I.25, B:I.25, B:K.29, B:L.31, B:I.47, B:V.51, B:V.51, B:A.57, B:V.77, C:A.12 Hydrogen bonds: B:T.30, B:N.39 Water bridges: B:Q.50 Salt bridges: B:K.29, B:K.55 Metal complexes: B:H.18 HEM.4: 25 residues within 4Å: Chain A: A.12 Chain C: N.13, C.14, C.17, H.18, N.23, I.25, M.26, K.29, T.30, L.31, A.35, L.36, N.39, M.41, I.47, Q.50, V.51, K.55, N.56, M.58, P.59, F.61, V.73, V.77 18 PLIP interactions: 17 interactions with chain C, 1 interactions with chain A, Hydrophobic interactions: C:I.25, C:I.25, C:K.29, C:L.31, C:I.47, C:V.51, C:M.58, C:F.61, C:V.73, C:V.77, A:A.12 Hydrogen bonds: C:T.30, C:N.39 Water bridges: C:K.29, C:K.29 Salt bridges: C:K.29, C:K.55 Metal complexes: C:H.18 HEM.5: 24 residues within 4Å: Chain B: V.24 Chain D: N.13, C.14, C.17, H.18, N.23, I.25, K.29, T.30, L.31, A.35, L.36, N.39, M.41, I.47, Q.50, V.51, K.55, N.56, A.57, M.58, P.59, F.61, V.77 20 PLIP interactions: 20 interactions with chain D, Hydrophobic interactions: D:I.25, D:K.29, D:L.31, D:L.36, D:I.47, D:V.51, D:A.57, D:F.61, D:F.61, D:V.77 Hydrogen bonds: D:T.30, D:N.39, D:N.56 Water bridges: D:K.29, D:K.29, D:Q.50, D:A.57 Salt bridges: D:K.29, D:K.55 Metal complexes: D:H.18 HEM.7: 25 residues within 4Å: Chain C: V.24 Chain E: N.13, C.14, C.17, H.18, N.23, I.25, M.26, K.29, T.30, L.31, A.35, L.36, N.39, M.41, I.47, Q.50, V.51, K.55, N.56, A.57, M.58, P.59, F.61, V.77 16 PLIP interactions: 15 interactions with chain E, 1 interactions with chain C, Hydrophobic interactions: E:I.25, E:K.29, E:L.31, E:I.47, E:V.51, E:A.57, E:F.61, E:F.61, E:V.77, C:V.24 Hydrogen bonds: E:T.30, E:N.39 Water bridges: E:K.29, E:K.29 Salt bridges: E:K.29 Metal complexes: E:H.18 HEM.9: 26 residues within 4Å: Chain A: V.24 Chain F: N.13, C.14, C.17, H.18, N.23, I.25, M.26, K.29, T.30, L.31, A.35, L.36, N.39, M.41, I.47, Q.50, V.51, K.55, N.56, A.57, M.58, P.59, F.61, V.73, V.77 15 PLIP interactions: 15 interactions with chain F, Hydrophobic interactions: F:I.25, F:I.25, F:K.29, F:L.31, F:I.47, F:V.51, F:A.57, F:V.73, F:V.77 Hydrogen bonds: F:T.30, F:N.39 Water bridges: F:A.57 Salt bridges: F:K.29, F:K.55 Metal complexes: F:H.18

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

SO4.2: 6 residues within 4Å: Chain A: G.63, R.64 Chain B: G.63, R.64 Chain C: G.63, R.64 6 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C, 2 interactions with chain B Water bridges: A:G.63, A:R.64, C:G.63, C:R.64, B:G.63 Hydrogen bonds: B:R.64 SO4.6: 2 residues within 4Å: Chain D: S.66, D.67 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.67 Water bridges: D:D.68 SO4.8: 5 residues within 4Å: Chain A: G.20, W.85 Chain E: M.26, P.27, E.28 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:E.28 Water bridges: A:G.20 SO4.10: 5 residues within 4Å: Chain B: G.20, W.85 Chain F: M.26, P.27, E.28 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:E.28, F:E.28 Water bridges: F:E.28, B:G.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Akazaki, H. et al., Cloning, expression and purification of cytochrome c(6) from the brown alga Hizikia fusiformis and complete X-ray diffraction analysis of the structure. ACTA CRYSTALLOGR.,SECT.F (2008)

Release Date

2008-09-30

Peptides

Cytochrome c6: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

D
G

E
I

F
K

Cytochrome c6

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