SMTL ID : 1mdv.3 (2 other biounits)

KEY ROLE OF PHENYLALANINE 20 IN CYTOCHROME C3: STRUCTURE, STABILITY AND FUNCTION STUDIES

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-octamer

Ligands

32 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.1: 16 residues within 4Å: Chain A: L.9, M.11, L.20, H.22, H.25, V.28, K.29, C.30, C.33, H.34, Y.43, K.45 Chain F: L.9, H.22 Ligands: HEM.3, HEM.21 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain F, Hydrophobic interactions: A:V.28, A:Y.43, A:Y.43, F:L.9 Hydrogen bonds: A:C.46 Salt bridges: A:K.45 Metal complexes: A:H.22, A:H.34 HEM.2: 16 residues within 4Å: Chain A: C.33, H.34, H.35, V.37, D.42, R.44, K.45, C.46, C.51, H.52, H.67, V.68, M.69, T.74, K.75, F.76 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:V.37, A:V.68 Hydrogen bonds: A:K.75 Salt bridges: A:H.67, A:K.75 pi-Stacking: A:F.76 Metal complexes: A:H.35, A:H.52 HEM.3: 9 residues within 4Å: Chain A: L.20, H.25, K.77, S.78, C.79, C.82, H.83, K.104 Ligands: HEM.1 6 PLIP interactions: 6 interactions with chain A, Hydrophobic interactions: A:L.20 Water bridges: A:N.21 Salt bridges: A:K.93, A:K.104 Metal complexes: A:H.25, A:H.83 HEM.4: 19 residues within 4Å: Chain A: M.11, Q.16, P.17, V.18, Y.65, Y.66, H.70, C.79, H.83, L.97, T.98, C.100, S.103, C.105, H.106 Chain B: P.17, C.100, H.106 Ligands: HEM.8 5 PLIP interactions: 5 interactions with chain A, Hydrophobic interactions: A:V.18, A:V.18 Hydrogen bonds: A:P.17 Metal complexes: A:H.70, A:H.106 HEM.5: 15 residues within 4Å: Chain B: L.9, M.11, H.22, H.25, C.30, C.33, H.34, Y.43, R.44, K.45, C.46 Chain G: H.22, K.26 Ligands: HEM.7, HEM.25 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain G, Hydrophobic interactions: B:Y.43, B:Y.43, G:K.26 Hydrogen bonds: B:Y.43, B:K.45 Water bridges: B:L.20, B:C.46 Salt bridges: B:K.45, B:K.45 Metal complexes: B:H.22, B:H.34 HEM.6: 14 residues within 4Å: Chain B: C.33, H.34, H.35, V.37, R.44, K.45, C.46, C.51, H.52, H.67, T.74, K.75, F.76, K.77 7 PLIP interactions: 7 interactions with chain B, Hydrophobic interactions: B:V.37, B:F.76 Hydrogen bonds: B:K.75 Salt bridges: B:H.67, B:K.75 Metal complexes: B:H.35, B:H.52 HEM.7: 10 residues within 4Å: Chain B: H.25, C.33, K.77, S.78, C.79, C.82, H.83, V.86, K.104 Ligands: HEM.5 7 PLIP interactions: 7 interactions with chain B, Hydrophobic interactions: B:K.77, B:V.86 Salt bridges: B:K.93, B:K.104 pi-Stacking: B:H.83 Metal complexes: B:H.25, B:H.83 HEM.8: 17 residues within 4Å: Chain A: K.15, Q.16, P.17, C.100, H.106 Chain B: M.11, Q.16, V.18, Y.65, H.70, C.79, H.83, L.97, C.100, C.105, H.106 Ligands: HEM.4 6 PLIP interactions: 6 interactions with chain B, Hydrophobic interactions: B:V.18 Hydrogen bonds: B:Q.16, B:Y.65, B:Y.65 Metal complexes: B:H.70, B:H.106 HEM.9: 16 residues within 4Å: Chain C: L.9, M.11, L.20, H.22, H.25, V.28, K.29, C.30, C.33, H.34, Y.43, K.45 Chain H: L.9, H.22 Ligands: HEM.11, HEM.29 8 PLIP interactions: 1 interactions with chain H, 7 interactions with chain C, Hydrophobic interactions: H:L.9, C:V.28, C:Y.43, C:Y.43 Hydrogen bonds: C:C.46 Salt bridges: C:K.45 Metal complexes: C:H.22, C:H.34 HEM.10: 16 residues within 4Å: Chain C: C.33, H.34, H.35, V.37, D.42, R.44, K.45, C.46, C.51, H.52, H.67, V.68, M.69, T.74, K.75, F.76 8 PLIP interactions: 8 interactions with chain C, Hydrophobic interactions: C:V.37, C:V.68 Hydrogen bonds: C:K.75 Salt bridges: C:H.67, C:K.75 pi-Stacking: C:F.76 Metal complexes: C:H.35, C:H.52 HEM.11: 9 residues within 4Å: Chain C: L.20, H.25, K.77, S.78, C.79, C.82, H.83, K.104 Ligands: HEM.9 6 PLIP interactions: 6 interactions with chain C, Hydrophobic interactions: C:L.20 Water bridges: C:N.21 Salt bridges: C:K.93, C:K.104 Metal complexes: C:H.25, C:H.83 HEM.12: 19 residues within 4Å: Chain C: M.11, Q.16, P.17, V.18, Y.65, Y.66, H.70, C.79, H.83, L.97, T.98, C.100, S.103, C.105, H.106 Chain D: P.17, C.100, H.106 Ligands: HEM.16 5 PLIP interactions: 5 interactions with chain C, Hydrophobic interactions: C:V.18, C:V.18 Hydrogen bonds: C:P.17 Metal complexes: C:H.70, C:H.106 HEM.13: 15 residues within 4Å: Chain D: L.9, M.11, H.22, H.25, C.30, C.33, H.34, Y.43, R.44, K.45, C.46 Chain E: H.22, K.26 Ligands: HEM.15, HEM.17 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain E, Hydrophobic interactions: D:Y.43, D:Y.43, E:K.26 Hydrogen bonds: D:Y.43, D:K.45 Water bridges: D:L.20, D:C.46 Salt bridges: D:K.45, D:K.45 Metal complexes: D:H.22, D:H.34 HEM.14: 14 residues within 4Å: Chain D: C.33, H.34, H.35, V.37, R.44, K.45, C.46, C.51, H.52, H.67, T.74, K.75, F.76, K.77 7 PLIP interactions: 7 interactions with chain D, Hydrophobic interactions: D:V.37, D:F.76 Hydrogen bonds: D:K.75 Salt bridges: D:H.67, D:K.75 Metal complexes: D:H.35, D:H.52 HEM.15: 10 residues within 4Å: Chain D: H.25, C.33, K.77, S.78, C.79, C.82, H.83, V.86, K.104 Ligands: HEM.13 7 PLIP interactions: 7 interactions with chain D, Hydrophobic interactions: D:K.77, D:V.86 Salt bridges: D:K.93, D:K.104 pi-Stacking: D:H.83 Metal complexes: D:H.25, D:H.83 HEM.16: 17 residues within 4Å: Chain C: K.15, Q.16, P.17, C.100, H.106 Chain D: M.11, Q.16, V.18, Y.65, H.70, C.79, H.83, L.97, C.100, C.105, H.106 Ligands: HEM.12 6 PLIP interactions: 6 interactions with chain D, Hydrophobic interactions: D:V.18 Hydrogen bonds: D:Q.16, D:Y.65, D:Y.65 Metal complexes: D:H.70, D:H.106 HEM.17: 16 residues within 4Å: Chain D: L.9, H.22 Chain E: L.9, M.11, L.20, H.22, H.25, V.28, K.29, C.30, C.33, H.34, Y.43, K.45 Ligands: HEM.13, HEM.19 8 PLIP interactions: 7 interactions with chain E, 1 interactions with chain D, Hydrophobic interactions: E:V.28, E:Y.43, E:Y.43, D:L.9 Hydrogen bonds: E:C.46 Salt bridges: E:K.45 Metal complexes: E:H.22, E:H.34 HEM.18: 16 residues within 4Å: Chain E: C.33, H.34, H.35, V.37, D.42, R.44, K.45, C.46, C.51, H.52, H.67, V.68, M.69, T.74, K.75, F.76 8 PLIP interactions: 8 interactions with chain E, Hydrophobic interactions: E:V.37, E:V.68 Hydrogen bonds: E:K.75 Salt bridges: E:H.67, E:K.75 pi-Stacking: E:F.76 Metal complexes: E:H.35, E:H.52 HEM.19: 9 residues within 4Å: Chain E: L.20, H.25, K.77, S.78, C.79, C.82, H.83, K.104 Ligands: HEM.17 6 PLIP interactions: 6 interactions with chain E, Hydrophobic interactions: E:L.20 Water bridges: E:N.21 Salt bridges: E:K.93, E:K.104 Metal complexes: E:H.25, E:H.83 HEM.20: 19 residues within 4Å: Chain E: M.11, Q.16, P.17, V.18, Y.65, Y.66, H.70, C.79, H.83, L.97, T.98, C.100, S.103, C.105, H.106 Chain F: P.17, C.100, H.106 Ligands: HEM.24 5 PLIP interactions: 5 interactions with chain E, Hydrophobic interactions: E:V.18, E:V.18 Hydrogen bonds: E:P.17 Metal complexes: E:H.70, E:H.106 HEM.21: 15 residues within 4Å: Chain A: H.22, K.26 Chain F: L.9, M.11, H.22, H.25, C.30, C.33, H.34, Y.43, R.44, K.45, C.46 Ligands: HEM.1, HEM.23 11 PLIP interactions: 10 interactions with chain F, 1 interactions with chain A, Hydrophobic interactions: F:Y.43, F:Y.43, A:K.26 Hydrogen bonds: F:Y.43, F:K.45 Water bridges: F:L.20, F:C.46 Salt bridges: F:K.45, F:K.45 Metal complexes: F:H.22, F:H.34 HEM.22: 14 residues within 4Å: Chain F: C.33, H.34, H.35, V.37, R.44, K.45, C.46, C.51, H.52, H.67, T.74, K.75, F.76, K.77 7 PLIP interactions: 7 interactions with chain F, Hydrophobic interactions: F:V.37, F:F.76 Hydrogen bonds: F:K.75 Salt bridges: F:H.67, F:K.75 Metal complexes: F:H.35, F:H.52 HEM.23: 10 residues within 4Å: Chain F: H.25, C.33, K.77, S.78, C.79, C.82, H.83, V.86, K.104 Ligands: HEM.21 7 PLIP interactions: 7 interactions with chain F, Hydrophobic interactions: F:K.77, F:V.86 Salt bridges: F:K.93, F:K.104 pi-Stacking: F:H.83 Metal complexes: F:H.25, F:H.83 HEM.24: 17 residues within 4Å: Chain E: K.15, Q.16, P.17, C.100, H.106 Chain F: M.11, Q.16, V.18, Y.65, H.70, C.79, H.83, L.97, C.100, C.105, H.106 Ligands: HEM.20 6 PLIP interactions: 6 interactions with chain F, Hydrophobic interactions: F:V.18 Hydrogen bonds: F:Q.16, F:Y.65, F:Y.65 Metal complexes: F:H.70, F:H.106 HEM.25: 16 residues within 4Å: Chain B: L.9, H.22 Chain G: L.9, M.11, L.20, H.22, H.25, V.28, K.29, C.30, C.33, H.34, Y.43, K.45 Ligands: HEM.5, HEM.27 8 PLIP interactions: 7 interactions with chain G, 1 interactions with chain B, Hydrophobic interactions: G:V.28, G:Y.43, G:Y.43, B:L.9 Hydrogen bonds: G:C.46 Salt bridges: G:K.45 Metal complexes: G:H.22, G:H.34 HEM.26: 16 residues within 4Å: Chain G: C.33, H.34, H.35, V.37, D.42, R.44, K.45, C.46, C.51, H.52, H.67, V.68, M.69, T.74, K.75, F.76 8 PLIP interactions: 8 interactions with chain G, Hydrophobic interactions: G:V.37, G:V.68 Hydrogen bonds: G:K.75 Salt bridges: G:H.67, G:K.75 pi-Stacking: G:F.76 Metal complexes: G:H.35, G:H.52 HEM.27: 9 residues within 4Å: Chain G: L.20, H.25, K.77, S.78, C.79, C.82, H.83, K.104 Ligands: HEM.25 6 PLIP interactions: 6 interactions with chain G, Hydrophobic interactions: G:L.20 Water bridges: G:N.21 Salt bridges: G:K.93, G:K.104 Metal complexes: G:H.25, G:H.83 HEM.28: 19 residues within 4Å: Chain G: M.11, Q.16, P.17, V.18, Y.65, Y.66, H.70, C.79, H.83, L.97, T.98, C.100, S.103, C.105, H.106 Chain H: P.17, C.100, H.106 Ligands: HEM.32 5 PLIP interactions: 5 interactions with chain G, Hydrophobic interactions: G:V.18, G:V.18 Hydrogen bonds: G:P.17 Metal complexes: G:H.70, G:H.106 HEM.29: 15 residues within 4Å: Chain C: H.22, K.26 Chain H: L.9, M.11, H.22, H.25, C.30, C.33, H.34, Y.43, R.44, K.45, C.46 Ligands: HEM.9, HEM.31 11 PLIP interactions: 1 interactions with chain C, 10 interactions with chain H, Hydrophobic interactions: C:K.26, H:Y.43, H:Y.43 Hydrogen bonds: H:Y.43, H:K.45 Water bridges: H:L.20, H:C.46 Salt bridges: H:K.45, H:K.45 Metal complexes: H:H.22, H:H.34 HEM.30: 14 residues within 4Å: Chain H: C.33, H.34, H.35, V.37, R.44, K.45, C.46, C.51, H.52, H.67, T.74, K.75, F.76, K.77 7 PLIP interactions: 7 interactions with chain H, Hydrophobic interactions: H:V.37, H:F.76 Hydrogen bonds: H:K.75 Salt bridges: H:H.67, H:K.75 Metal complexes: H:H.35, H:H.52 HEM.31: 10 residues within 4Å: Chain H: H.25, C.33, K.77, S.78, C.79, C.82, H.83, V.86, K.104 Ligands: HEM.29 7 PLIP interactions: 7 interactions with chain H, Hydrophobic interactions: H:K.77, H:V.86 Salt bridges: H:K.93, H:K.104 pi-Stacking: H:H.83 Metal complexes: H:H.25, H:H.83 HEM.32: 17 residues within 4Å: Chain G: K.15, Q.16, P.17, C.100, H.106 Chain H: M.11, Q.16, V.18, Y.65, H.70, C.79, H.83, L.97, C.100, C.105, H.106 Ligands: HEM.28 6 PLIP interactions: 6 interactions with chain H, Hydrophobic interactions: H:V.18 Hydrogen bonds: H:Q.16, H:Y.65, H:Y.65 Metal complexes: H:H.70, H:H.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dolla, A. et al., Key role of phenylalanine 20 in cytochrome c3: structure, stability, and function studies. Biochemistry (1999)

Release Date

1999-05-04

Peptides

CYTOCHROME C3: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

CYTOCHROME C3

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