SMTL ID : 1duw.2 (1 other biounit)

STRUCTURE OF NONAHEME CYTOCHROME C

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-dimer

Ligands

18 x HEC: HEME C(Covalent)

HEC.1: 22 residues within 4Å: Chain A: C.50, H.51, H.52, T.53, V.57, A.58, C.59, T.61, C.62, H.63, E.70, G.71, N.72, V.74, R.78, A.79, M.80, I.85, R.88, P.94, V.95, S.96 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:T.53, A:V.57, A:V.74, A:A.79, A:P.94, A:P.94 Water bridges: A:R.88, A:R.88 Salt bridges: A:R.78, A:R.88, A:R.88 pi-Stacking: A:H.63, A:H.63 Metal complexes: A:H.52, A:H.63 HEC.2: 26 residues within 4Å: Chain A: M.16, F.17, P.18, A.29, M.30, K.31, P.32, A.33, L.76, M.80, H.81, C.97, V.98, H.101, R.122, W.126, C.127, C.130, H.131 Chain B: R.231, S.232, P.239, S.243, C.244 Ligands: HEC.5, HEC.16 20 PLIP interactions: 3 interactions with chain B, 17 interactions with chain A, Hydrophobic interactions: B:P.239, A:M.16, A:P.18, A:A.33, A:L.76, A:M.80, A:V.98, A:W.126, A:W.126, A:W.126 Hydrogen bonds: B:S.243, B:S.243, A:M.30, A:A.33 Water bridges: A:N.24 Salt bridges: A:H.131 pi-Stacking: A:H.81, A:H.81 Metal complexes: A:H.81, A:H.131 HEC.3: 21 residues within 4Å: Chain A: T.105, R.108, E.110, C.111, C.114, H.115, V.118, P.120, K.121, R.122, W.126, L.204, I.208, D.211, L.213, A.214, F.217, H.218, T.223, L.224, T.227 23 PLIP interactions: 23 interactions with chain A, Hydrophobic interactions: A:T.105, A:E.110, A:V.118, A:V.118, A:P.120, A:L.204, A:I.208, A:D.211, A:L.213, A:A.214, A:F.217, A:F.217, A:T.223, A:T.227 Hydrogen bonds: A:K.121 Water bridges: A:R.122, A:R.122 Salt bridges: A:R.122 pi-Stacking: A:H.115, A:H.115, A:H.218 Metal complexes: A:H.115, A:H.218 HEC.4: 16 residues within 4Å: Chain A: S.8, A.10, I.14, M.16, F.35, H.37, H.40, I.44, C.47, C.50, H.51, P.56, V.57, A.58, C.59 Ligands: HEC.5 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:A.10, A:F.35, A:F.35, A:H.40, A:I.44, A:P.56 Hydrogen bonds: A:A.58, A:C.59 pi-Stacking: A:H.51, A:H.51 Metal complexes: A:H.37, A:H.51 HEC.5: 21 residues within 4Å: Chain A: M.16, F.35, N.36, A.39, H.40, K.43, I.44, T.49, C.50, V.95, S.96, C.97, C.100, H.101, Q.104, T.129, K.212, L.213, A.216 Ligands: HEC.2, HEC.4 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:F.35, A:K.43, A:I.44, A:T.49, A:V.95, A:L.213, A:L.213, A:A.216 Water bridges: A:N.36, A:N.36, A:K.212, A:K.212 Salt bridges: A:K.43, A:K.212 pi-Stacking: A:F.35, A:H.101 Metal complexes: A:H.40, A:H.101 HEC.6: 17 residues within 4Å: Chain A: T.119, C.228, H.229, H.230, R.231, P.239, K.240, C.241, C.244, H.245, N.255, R.256, P.257, A.262, L.265, Q.266 Ligands: HEC.12 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:R.256, A:P.257, A:A.262, A:L.265 Hydrogen bonds: A:T.119, A:N.255 Water bridges: A:R.231, A:R.231, A:Q.266 Salt bridges: A:H.230, A:R.231, A:R.231 pi-Stacking: A:H.230, A:H.230, A:H.245 Metal complexes: A:H.230, A:H.245 HEC.7: 22 residues within 4Å: Chain A: I.183, D.184, A.185, L.186, A.187, D.188, K.189, Y.190, S.193, K.260, Y.263, H.264, C.267, M.268, H.271, K.280, N.281, D.283, C.284, C.287, H.288 Ligands: HEC.9 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:I.183, A:L.186, A:K.260, A:Y.263, A:Y.263 Hydrogen bonds: A:L.186, A:A.187, A:D.188, A:K.189, A:Y.190 Water bridges: A:D.188, A:Y.190 Metal complexes: A:H.264, A:H.288 HEC.8: 18 residues within 4Å: Chain A: L.172, Q.176, G.177, P.178, V.181, I.183, F.195, H.197, M.201, L.224, C.225, C.228, H.229, A.236, K.240, C.241, Y.263 Ligands: HEC.9 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:L.172, A:L.172, A:I.183, A:F.195 Hydrogen bonds: A:C.241 Water bridges: A:K.240, A:K.240, A:K.240, A:G.242 Salt bridges: A:K.240, B:K.26 pi-Stacking: A:H.197 pi-Cation interactions: A:H.197 Metal complexes: A:H.197, A:H.229 HEC.9: 24 residues within 4Å: Chain A: C.114, I.117, I.183, S.193, F.195, T.196, R.199, H.200, S.203, L.204, R.207, C.228, Q.266, C.267, C.270, H.271, M.274, V.276, R.278, P.279, T.286, C.287 Ligands: HEC.7, HEC.8 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:I.117, A:I.183, A:F.195, A:F.195, A:L.204, A:V.276, A:V.276 Hydrogen bonds: A:S.203 Water bridges: A:T.196, A:R.207, A:R.207, A:R.207 Salt bridges: A:R.199, A:R.199, A:H.200, A:R.207 Metal complexes: A:H.200, A:H.271 HEC.11: 22 residues within 4Å: Chain B: C.50, H.51, H.52, T.53, V.57, A.58, C.59, T.61, C.62, H.63, E.70, G.71, N.72, V.74, R.78, A.79, M.80, I.85, R.88, P.94, V.95, S.96 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:T.53, B:V.57, B:V.74, B:A.79, B:P.94, B:P.94 Water bridges: B:R.88, B:R.88 Salt bridges: B:R.78, B:R.88, B:R.88 pi-Stacking: B:H.63, B:H.63 Metal complexes: B:H.52, B:H.63 HEC.12: 26 residues within 4Å: Chain A: R.231, S.232, P.239, S.243, C.244 Chain B: M.16, F.17, P.18, A.29, M.30, K.31, P.32, A.33, L.76, M.80, H.81, C.97, V.98, H.101, R.122, W.126, C.127, C.130, H.131 Ligands: HEC.6, HEC.15 20 PLIP interactions: 17 interactions with chain B, 3 interactions with chain A, Hydrophobic interactions: B:M.16, B:P.18, B:A.33, B:L.76, B:M.80, B:V.98, B:W.126, B:W.126, B:W.126, A:P.239 Hydrogen bonds: B:M.30, B:A.33, A:S.243, A:S.243 Water bridges: B:N.24 Salt bridges: B:H.131 pi-Stacking: B:H.81, B:H.81 Metal complexes: B:H.81, B:H.131 HEC.13: 21 residues within 4Å: Chain B: T.105, R.108, E.110, C.111, C.114, H.115, V.118, P.120, K.121, R.122, W.126, L.204, I.208, D.211, L.213, A.214, F.217, H.218, T.223, L.224, T.227 23 PLIP interactions: 23 interactions with chain B, Hydrophobic interactions: B:T.105, B:E.110, B:V.118, B:V.118, B:P.120, B:L.204, B:I.208, B:D.211, B:L.213, B:A.214, B:F.217, B:F.217, B:T.223, B:T.227 Hydrogen bonds: B:K.121 Water bridges: B:R.122, B:R.122 Salt bridges: B:R.122 pi-Stacking: B:H.115, B:H.115, B:H.218 Metal complexes: B:H.115, B:H.218 HEC.14: 16 residues within 4Å: Chain B: S.8, A.10, I.14, M.16, F.35, H.37, H.40, I.44, C.47, C.50, H.51, P.56, V.57, A.58, C.59 Ligands: HEC.15 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:A.10, B:F.35, B:F.35, B:H.40, B:I.44, B:P.56 Hydrogen bonds: B:A.58, B:C.59 pi-Stacking: B:H.51, B:H.51 Metal complexes: B:H.37, B:H.51 HEC.15: 21 residues within 4Å: Chain B: M.16, F.35, N.36, A.39, H.40, K.43, I.44, T.49, C.50, V.95, S.96, C.97, C.100, H.101, Q.104, T.129, K.212, L.213, A.216 Ligands: HEC.12, HEC.14 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:F.35, B:K.43, B:I.44, B:T.49, B:V.95, B:L.213, B:L.213, B:A.216 Water bridges: B:N.36, B:N.36, B:K.212, B:K.212 Salt bridges: B:K.43, B:K.212 pi-Stacking: B:F.35, B:H.101 Metal complexes: B:H.40, B:H.101 HEC.16: 17 residues within 4Å: Chain B: T.119, C.228, H.229, H.230, R.231, P.239, K.240, C.241, C.244, H.245, N.255, R.256, P.257, A.262, L.265, Q.266 Ligands: HEC.2 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:R.256, B:P.257, B:A.262, B:L.265 Hydrogen bonds: B:N.255 Water bridges: B:R.231, B:R.231, B:Q.266 Salt bridges: B:H.230, B:R.231, B:R.231 pi-Stacking: B:H.230, B:H.230, B:H.245 Metal complexes: B:H.230, B:H.245 HEC.17: 22 residues within 4Å: Chain B: I.183, D.184, A.185, L.186, A.187, D.188, K.189, Y.190, S.193, K.260, Y.263, H.264, C.267, M.268, H.271, K.280, N.281, D.283, C.284, C.287, H.288 Ligands: HEC.19 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:I.183, B:L.186, B:K.260, B:Y.263, B:Y.263 Hydrogen bonds: B:L.186, B:A.187, B:D.188, B:K.189, B:Y.190 Water bridges: B:Y.190 Metal complexes: B:H.264, B:H.288 HEC.18: 18 residues within 4Å: Chain B: L.172, Q.176, G.177, P.178, V.181, I.183, F.195, H.197, M.201, L.224, C.225, C.228, H.229, A.236, K.240, C.241, Y.263 Ligands: HEC.19 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:L.172, B:L.172, B:I.183, B:F.195 Hydrogen bonds: B:C.241, B:Y.263 Water bridges: B:K.240, B:K.240, B:K.240, B:G.242 Salt bridges: B:K.240, A:K.26 pi-Stacking: B:H.197 pi-Cation interactions: B:H.197 Metal complexes: B:H.197, B:H.229 HEC.19: 24 residues within 4Å: Chain B: C.114, I.117, I.183, S.193, F.195, T.196, R.199, H.200, S.203, L.204, R.207, C.228, Q.266, C.267, C.270, H.271, M.274, V.276, R.278, P.279, T.286, C.287 Ligands: HEC.17, HEC.18 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:I.117, B:I.183, B:F.195, B:F.195, B:L.204, B:V.276, B:V.276 Hydrogen bonds: B:T.196, B:S.203 Water bridges: B:T.196, B:R.207, B:R.207, B:R.207 Salt bridges: B:R.199, B:R.199, B:H.200, B:R.207 Metal complexes: B:H.200, B:H.271

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 7 residues within 4Å: Chain A: G.27, A.29, M.30, K.31, P.32, M.142 Chain B: T.237 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.27, A:A.29, A:K.31, A:K.31, B:T.237 Water bridges: B:S.235 GOL.20: 7 residues within 4Å: Chain A: T.237 Chain B: G.27, A.29, M.30, K.31, P.32, M.142 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.27, B:A.29, B:K.31, B:K.31 Water bridges: A:S.235

Links

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Citation

Umhau, S. et al., Three-dimensional structure of the nonaheme cytochrome c from Desulfovibrio desulfuricans Essex in the Fe(III) state at 1.89 A resolution. Biochemistry (2001)

Release Date

2001-03-21

Peptides

NONAHEME CYTOCHROME C: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

NONAHEME CYTOCHROME C

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