SMTL ID : 1ci3.2 (2 other biounits)

CYTOCHROME F FROM THE B6F COMPLEX OF PHORMIDIUM LAMINOSUM

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-hexamer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: Y.53, H.55, E.125 Chain D: D.54, S.56 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: A:H.55, A:E.125, A:E.125, D:D.54, H2O.1 ZN.2: 3 residues within 4Å: Chain A: H.150 Chain B: E.198, D.199 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:D.199, A:H.150, H2O.1 ZN.4: 5 residues within 4Å: Chain B: Y.53, H.55, E.125 Chain F: D.54, S.56 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: B:H.55, B:E.125, B:E.125, F:D.54, H2O.10 ZN.5: 3 residues within 4Å: Chain B: H.150 Chain C: E.198, D.199 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:H.150, C:D.199, H2O.11 ZN.7: 5 residues within 4Å: Chain C: Y.53, H.55, E.125 Chain E: D.54, S.56 5 PLIP interactions: 1 interactions with chain E, 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: E:D.54, C:H.55, C:E.125, C:E.125, H2O.20 ZN.8: 3 residues within 4Å: Chain A: E.198, D.199 Chain C: H.150 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: C:H.150, A:D.199, H2O.20 ZN.10: 5 residues within 4Å: Chain A: D.54, S.56 Chain D: Y.53, H.55, E.125 5 PLIP interactions: 1 interactions with chain A, 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: A:D.54, D:H.55, D:E.125, D:E.125, H2O.29 ZN.11: 3 residues within 4Å: Chain D: H.150 Chain E: E.198, D.199 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: E:D.199, D:H.150, H2O.30 ZN.13: 5 residues within 4Å: Chain C: D.54, S.56 Chain E: Y.53, H.55, E.125 5 PLIP interactions: 1 interactions with chain C, 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: C:D.54, E:H.55, E:E.125, E:E.125, H2O.39 ZN.14: 3 residues within 4Å: Chain E: H.150 Chain F: E.198, D.199 3 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: F:D.199, E:H.150, H2O.40 ZN.16: 5 residues within 4Å: Chain B: D.54, S.56 Chain F: Y.53, H.55, E.125 5 PLIP interactions: 3 interactions with chain F, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: F:H.55, F:E.125, F:E.125, B:D.54, H2O.49 ZN.17: 3 residues within 4Å: Chain D: E.198, D.199 Chain F: H.150 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: D:D.199, F:H.150, H2O.49

6 x HEC: HEME C(Covalent)

HEC.3: 23 residues within 4Å: Chain A: Y.1, P.2, W.4, A.5, Y.9, C.21, C.24, H.25, Q.59, L.69, N.70, V.71, G.72, A.73, V.74, P.118, N.154, G.156, R.157, G.158, I.160, Y.161, P.162 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:Y.1, A:Y.1, A:W.4, A:W.4, A:A.5, A:Y.9, A:N.70, A:V.74, A:N.154, A:R.157, A:Y.161, A:Y.161 Hydrogen bonds: A:Y.1, A:Q.59, A:N.70, A:N.70, A:G.156, A:Y.161 Water bridges: A:A.62 Salt bridges: A:R.157 pi-Stacking: A:W.4 Metal complexes: A:H.25 HEC.6: 23 residues within 4Å: Chain B: Y.1, P.2, W.4, A.5, Y.9, C.21, C.24, H.25, Q.59, L.69, N.70, V.71, G.72, A.73, V.74, P.118, N.154, G.156, R.157, G.158, I.160, Y.161, P.162 22 PLIP interactions: 22 interactions with chain B, Hydrophobic interactions: B:Y.1, B:Y.1, B:W.4, B:W.4, B:A.5, B:Y.9, B:N.70, B:V.74, B:N.154, B:R.157, B:Y.161, B:Y.161 Hydrogen bonds: B:Y.1, B:Q.59, B:N.70, B:N.70, B:G.156, B:Y.161 Water bridges: B:A.62 Salt bridges: B:R.157 pi-Stacking: B:W.4 Metal complexes: B:H.25 HEC.9: 23 residues within 4Å: Chain C: Y.1, P.2, W.4, A.5, Y.9, C.21, C.24, H.25, Q.59, L.69, N.70, V.71, G.72, A.73, V.74, P.118, N.154, G.156, R.157, G.158, I.160, Y.161, P.162 22 PLIP interactions: 22 interactions with chain C, Hydrophobic interactions: C:Y.1, C:Y.1, C:W.4, C:W.4, C:A.5, C:Y.9, C:N.70, C:V.74, C:N.154, C:R.157, C:Y.161, C:Y.161 Hydrogen bonds: C:Y.1, C:Q.59, C:N.70, C:N.70, C:G.156, C:Y.161 Water bridges: C:A.62 Salt bridges: C:R.157 pi-Stacking: C:W.4 Metal complexes: C:H.25 HEC.12: 23 residues within 4Å: Chain D: Y.1, P.2, W.4, A.5, Y.9, C.21, C.24, H.25, Q.59, L.69, N.70, V.71, G.72, A.73, V.74, P.118, N.154, G.156, R.157, G.158, I.160, Y.161, P.162 22 PLIP interactions: 22 interactions with chain D, Hydrophobic interactions: D:Y.1, D:Y.1, D:W.4, D:W.4, D:A.5, D:Y.9, D:N.70, D:V.74, D:N.154, D:R.157, D:Y.161, D:Y.161 Hydrogen bonds: D:Y.1, D:Q.59, D:N.70, D:N.70, D:G.156 Water bridges: D:Y.1, D:A.62 Salt bridges: D:R.157 pi-Stacking: D:W.4 Metal complexes: D:H.25 HEC.15: 23 residues within 4Å: Chain E: Y.1, P.2, W.4, A.5, Y.9, C.21, C.24, H.25, Q.59, L.69, N.70, V.71, G.72, A.73, V.74, P.118, N.154, G.156, R.157, G.158, I.160, Y.161, P.162 22 PLIP interactions: 22 interactions with chain E, Hydrophobic interactions: E:Y.1, E:Y.1, E:W.4, E:W.4, E:A.5, E:Y.9, E:N.70, E:V.74, E:N.154, E:R.157, E:Y.161, E:Y.161 Hydrogen bonds: E:Y.1, E:Q.59, E:N.70, E:N.70, E:G.156 Water bridges: E:Y.1, E:A.62 Salt bridges: E:R.157 pi-Stacking: E:W.4 Metal complexes: E:H.25 HEC.18: 23 residues within 4Å: Chain F: Y.1, P.2, W.4, A.5, Y.9, C.21, C.24, H.25, Q.59, L.69, N.70, V.71, G.72, A.73, V.74, P.118, N.154, G.156, R.157, G.158, I.160, Y.161, P.162 22 PLIP interactions: 22 interactions with chain F, Hydrophobic interactions: F:Y.1, F:Y.1, F:W.4, F:W.4, F:A.5, F:Y.9, F:N.70, F:V.74, F:N.154, F:R.157, F:Y.161, F:Y.161 Hydrogen bonds: F:Y.1, F:Q.59, F:N.70, F:N.70, F:G.156 Water bridges: F:Y.1, F:A.62 Salt bridges: F:R.157 pi-Stacking: F:W.4 Metal complexes: F:H.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carrell, C.J. et al., Structure of the soluble domain of cytochrome f from the cyanobacterium Phormidium laminosum. Biochemistry (1999)

Release Date

1999-08-11

Peptides

PROTEIN (CYTOCHROME F): ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
M

B
M

C
M

D
M

E
M

F
M

PROTEIN (CYTOCHROME F)

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