SMTL ID : 2v08.1

Structure of wild-type Phormidium laminosum cytochrome c6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

6 x HEC: HEME C(Covalent)

HEC.1: 27 residues within 4Å: Chain A: N.14, C.15, C.18, H.19, N.24, V.26, N.27, K.30, T.31, L.32, A.36, L.37, F.40, M.42, I.48, Q.51, V.52, K.56, A.57, G.58, M.59, P.60, F.62, V.74, V.78 Chain B: A.17, C.18 20 PLIP interactions: 1 interactions with chain B, 19 interactions with chain A, Hydrophobic interactions: B:A.17, A:V.26, A:K.30, A:L.32, A:L.37, A:I.48, A:V.52, A:M.59, A:P.60, A:F.62, A:F.62, A:V.74, A:V.78 Hydrogen bonds: A:N.27, A:T.31 Water bridges: A:Q.51, A:G.58 Salt bridges: A:K.30, A:K.56 Metal complexes: A:H.19 HEC.12: 25 residues within 4Å: Chain A: A.17 Chain B: N.14, C.15, C.18, H.19, N.24, V.26, N.27, K.30, T.31, L.32, A.36, L.37, F.40, M.42, I.48, Q.51, V.52, K.56, A.57, G.58, M.59, P.60, F.62, V.78 18 PLIP interactions: 17 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:V.26, B:V.26, B:K.30, B:L.32, B:I.48, B:V.52, B:K.56, B:M.59, B:F.62, B:V.78, A:A.17 Hydrogen bonds: B:N.27 Water bridges: B:K.30, B:K.30, B:G.58 Salt bridges: B:K.30, B:K.56 Metal complexes: B:H.19 HEC.19: 27 residues within 4Å: Chain C: N.14, C.15, C.18, H.19, N.24, V.26, N.27, K.30, T.31, L.32, A.36, L.37, F.40, M.42, I.48, Q.51, V.52, K.56, A.57, G.58, M.59, P.60, F.62, V.74, V.78 Chain D: A.17, C.18 20 PLIP interactions: 19 interactions with chain C, 1 interactions with chain D, Hydrophobic interactions: C:V.26, C:K.30, C:L.32, C:L.37, C:I.48, C:V.52, C:M.59, C:P.60, C:F.62, C:F.62, C:V.74, C:V.78, D:A.17 Hydrogen bonds: C:N.27, C:T.31 Water bridges: C:Q.51, C:G.58 Salt bridges: C:K.30, C:K.56 Metal complexes: C:H.19 HEC.30: 25 residues within 4Å: Chain C: A.17 Chain D: N.14, C.15, C.18, H.19, N.24, V.26, N.27, K.30, T.31, L.32, A.36, L.37, F.40, M.42, I.48, Q.51, V.52, K.56, A.57, G.58, M.59, P.60, F.62, V.78 18 PLIP interactions: 17 interactions with chain D, 1 interactions with chain C, Hydrophobic interactions: D:V.26, D:V.26, D:K.30, D:L.32, D:I.48, D:V.52, D:K.56, D:M.59, D:F.62, D:V.78, C:A.17 Hydrogen bonds: D:N.27 Water bridges: D:K.30, D:K.30, D:G.58 Salt bridges: D:K.30, D:K.56 Metal complexes: D:H.19 HEC.37: 27 residues within 4Å: Chain E: N.14, C.15, C.18, H.19, N.24, V.26, N.27, K.30, T.31, L.32, A.36, L.37, F.40, M.42, I.48, Q.51, V.52, K.56, A.57, G.58, M.59, P.60, F.62, V.74, V.78 Chain F: A.17, C.18 20 PLIP interactions: 1 interactions with chain F, 19 interactions with chain E, Hydrophobic interactions: F:A.17, E:V.26, E:K.30, E:L.32, E:L.37, E:I.48, E:V.52, E:M.59, E:P.60, E:F.62, E:F.62, E:V.74, E:V.78 Hydrogen bonds: E:N.27, E:T.31 Water bridges: E:Q.51, E:G.58 Salt bridges: E:K.30, E:K.56 Metal complexes: E:H.19 HEC.48: 25 residues within 4Å: Chain E: A.17 Chain F: N.14, C.15, C.18, H.19, N.24, V.26, N.27, K.30, T.31, L.32, A.36, L.37, F.40, M.42, I.48, Q.51, V.52, K.56, A.57, G.58, M.59, P.60, F.62, V.78 18 PLIP interactions: 17 interactions with chain F, 1 interactions with chain E, Hydrophobic interactions: F:V.26, F:V.26, F:K.30, F:L.32, F:I.48, F:V.52, F:K.56, F:M.59, F:F.62, F:V.78, E:A.17 Hydrogen bonds: F:N.27 Water bridges: F:K.30, F:K.30, F:G.58 Salt bridges: F:K.30, F:K.56 Metal complexes: F:H.19

12 x IMD: IMIDAZOLE(Non-covalent)

IMD.2: 10 residues within 4Å: Chain A: N.24, L.25, A.28 Chain E: I.23, L.25 Ligands: ZN.5, IMD.20, ZN.23, IMD.38, ZN.41 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.24 IMD.3: 8 residues within 4Å: Chain A: E.35 Chain E: Y.77, Q.81, W.86 Ligands: ZN.7, CL.9, CL.10, CL.11 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Q.81 Water bridges: E:Y.77 pi-Stacking: E:W.86 IMD.13: 10 residues within 4Å: Chain B: I.23, L.25 Chain F: N.24, L.25, A.28 Ligands: ZN.15, IMD.31, ZN.33, IMD.49, ZN.51 No protein-ligand interaction detected (PLIP) IMD.14: 6 residues within 4Å: Chain B: G.21, Y.77, Q.81, W.86 Chain F: E.35 Ligands: ZN.16 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:Y.77, B:Y.77, B:Q.81, F:E.35 Water bridges: B:G.21 IMD.20: 10 residues within 4Å: Chain A: I.23, L.25 Chain C: N.24, L.25, A.28 Ligands: IMD.2, ZN.5, ZN.23, IMD.38, ZN.41 1 PLIP interactions: 1 interactions with chain C Water bridges: C:N.24 IMD.21: 8 residues within 4Å: Chain A: Y.77, Q.81, W.86 Chain C: E.35 Ligands: ZN.25, CL.27, CL.28, CL.29 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.81 Water bridges: A:Y.77 pi-Stacking: A:W.86 IMD.31: 10 residues within 4Å: Chain B: N.24, L.25, A.28 Chain D: I.23, L.25 Ligands: IMD.13, ZN.15, ZN.33, IMD.49, ZN.51 No protein-ligand interaction detected (PLIP) IMD.32: 6 residues within 4Å: Chain B: E.35 Chain D: G.21, Y.77, Q.81, W.86 Ligands: ZN.34 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:Y.77, D:Y.77, D:Q.81, B:E.35 Water bridges: D:G.21 IMD.38: 10 residues within 4Å: Chain C: I.23, L.25 Chain E: N.24, L.25, A.28 Ligands: IMD.2, ZN.5, IMD.20, ZN.23, ZN.41 1 PLIP interactions: 1 interactions with chain E Water bridges: E:N.24 IMD.39: 8 residues within 4Å: Chain C: Y.77, Q.81, W.86 Chain E: E.35 Ligands: ZN.43, CL.45, CL.46, CL.47 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.81 Water bridges: C:Y.77 pi-Stacking: C:W.86 IMD.49: 10 residues within 4Å: Chain D: N.24, L.25, A.28 Chain F: I.23, L.25 Ligands: IMD.13, ZN.15, IMD.31, ZN.33, ZN.51 No protein-ligand interaction detected (PLIP) IMD.50: 6 residues within 4Å: Chain D: E.35 Chain F: G.21, Y.77, Q.81, W.86 Ligands: ZN.52 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain F Hydrogen bonds: D:E.35, F:Y.77, F:Y.77, F:Q.81 Water bridges: F:G.21

27 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.4: 2 residues within 4Å: Chain A: N.27, E.29 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.29, H2O.3, H2O.3 ZN.5: 5 residues within 4Å: Ligands: IMD.2, IMD.20, ZN.23, IMD.38, ZN.41 No protein-ligand interaction detected (PLIP) ZN.6: 2 residues within 4Å: Chain A: D.68, D.69 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.68, A:D.68, H2O.3 ZN.7: 5 residues within 4Å: Chain E: G.21 Ligands: IMD.3, CL.9, CL.10, CL.11 No protein-ligand interaction detected (PLIP) ZN.8: 2 residues within 4Å: Chain A: E.35 Chain E: W.86 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: A:E.35, E:W.86, H2O.3 ZN.15: 5 residues within 4Å: Ligands: IMD.13, IMD.31, ZN.33, IMD.49, ZN.51 No protein-ligand interaction detected (PLIP) ZN.16: 2 residues within 4Å: Chain B: G.21 Ligands: IMD.14 No protein-ligand interaction detected (PLIP) ZN.17: 2 residues within 4Å: Chain B: N.27, E.29 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.29, H2O.5, H2O.5 ZN.18: 2 residues within 4Å: Chain B: E.35 Chain D: W.86 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Metal complexes: D:W.86, B:E.35 ZN.22: 2 residues within 4Å: Chain C: N.27, E.29 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.29, H2O.7, H2O.7 ZN.23: 5 residues within 4Å: Ligands: IMD.2, ZN.5, IMD.20, IMD.38, ZN.41 No protein-ligand interaction detected (PLIP) ZN.24: 2 residues within 4Å: Chain C: D.68, D.69 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.68, C:D.68, H2O.8 ZN.25: 5 residues within 4Å: Chain A: G.21 Ligands: IMD.21, CL.27, CL.28, CL.29 No protein-ligand interaction detected (PLIP) ZN.26: 2 residues within 4Å: Chain A: W.86 Chain C: E.35 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: A:W.86, C:E.35, H2O.8 ZN.33: 5 residues within 4Å: Ligands: IMD.13, ZN.15, IMD.31, IMD.49, ZN.51 No protein-ligand interaction detected (PLIP) ZN.34: 2 residues within 4Å: Chain D: G.21 Ligands: IMD.32 No protein-ligand interaction detected (PLIP) ZN.35: 2 residues within 4Å: Chain D: N.27, E.29 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.29, H2O.9, H2O.9 ZN.36: 2 residues within 4Å: Chain D: E.35 Chain F: W.86 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F Metal complexes: D:E.35, F:W.86 ZN.40: 2 residues within 4Å: Chain E: N.27, E.29 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.29, H2O.12, H2O.12 ZN.41: 5 residues within 4Å: Ligands: IMD.2, ZN.5, IMD.20, ZN.23, IMD.38 No protein-ligand interaction detected (PLIP) ZN.42: 2 residues within 4Å: Chain E: D.68, D.69 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.68, E:D.68, H2O.12 ZN.43: 5 residues within 4Å: Chain C: G.21 Ligands: IMD.39, CL.45, CL.46, CL.47 No protein-ligand interaction detected (PLIP) ZN.44: 2 residues within 4Å: Chain C: W.86 Chain E: E.35 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: C:W.86, E:E.35, H2O.12 ZN.51: 5 residues within 4Å: Ligands: IMD.13, ZN.15, IMD.31, ZN.33, IMD.49 No protein-ligand interaction detected (PLIP) ZN.52: 2 residues within 4Å: Chain F: G.21 Ligands: IMD.50 No protein-ligand interaction detected (PLIP) ZN.53: 2 residues within 4Å: Chain F: N.27, E.29 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.29, H2O.14, H2O.14 ZN.54: 2 residues within 4Å: Chain B: W.86 Chain F: E.35 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain B Metal complexes: F:E.35, B:W.86

9 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 8 residues within 4Å: Chain A: T.31, K.33, A.36 Chain E: G.21 Ligands: IMD.3, ZN.7, CL.10, CL.11 Ligand excluded by PLIP CL.10: 8 residues within 4Å: Chain E: F.11, A.16, A.20, G.21 Ligands: IMD.3, ZN.7, CL.9, CL.11 Ligand excluded by PLIP CL.11: 7 residues within 4Å: Chain A: E.35, A.36, K.39 Ligands: IMD.3, ZN.7, CL.9, CL.10 Ligand excluded by PLIP CL.27: 8 residues within 4Å: Chain A: G.21 Chain C: T.31, K.33, A.36 Ligands: IMD.21, ZN.25, CL.28, CL.29 Ligand excluded by PLIP CL.28: 8 residues within 4Å: Chain A: F.11, A.16, A.20, G.21 Ligands: IMD.21, ZN.25, CL.27, CL.29 Ligand excluded by PLIP CL.29: 7 residues within 4Å: Chain C: E.35, A.36, K.39 Ligands: IMD.21, ZN.25, CL.27, CL.28 Ligand excluded by PLIP CL.45: 8 residues within 4Å: Chain C: G.21 Chain E: T.31, K.33, A.36 Ligands: IMD.39, ZN.43, CL.46, CL.47 Ligand excluded by PLIP CL.46: 8 residues within 4Å: Chain C: F.11, A.16, A.20, G.21 Ligands: IMD.39, ZN.43, CL.45, CL.47 Ligand excluded by PLIP CL.47: 7 residues within 4Å: Chain E: E.35, A.36, K.39 Ligands: IMD.39, ZN.43, CL.45, CL.46 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Worrall, J.A. et al., Modulation of heme redox potential in the cytochrome c6 family. J. Am. Chem. Soc. (2007)

Release Date

2007-07-24

Peptides

CYTOCHROME C6: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

CYTOCHROME C6