SMTL ID : 19hc.1

NINE-HAEM CYTOCHROME C FROM DESULFOVIBRIO DESULFURICANS ATCC 27774

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

5 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 4 residues within 4Å: Chain A: P.5, P.11, S.12, E.156 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.12 Water bridges: A:A.13 ACT.2: 8 residues within 4Å: Chain A: K.121, R.231, S.232, P.233 Chain B: D.122, E.124, C.127 Ligands: HEM.19 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Water bridges: B:E.124, A:K.121, A:K.121, A:L.234 Salt bridges: A:K.121 ACT.3: 4 residues within 4Å: Chain A: D.77, H.81, W.126 Ligands: HEM.8 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:H.81, A:W.126 Salt bridges: A:H.81 Water bridges: B:R.256 ACT.13: 8 residues within 4Å: Chain A: D.122, E.124, C.127 Chain B: K.121, R.231, S.232, P.233 Ligands: HEM.8 4 PLIP interactions: 4 interactions with chain B Water bridges: B:K.121, B:K.121, B:K.121 Salt bridges: B:K.121 ACT.14: 3 residues within 4Å: Chain B: M.260, A.261, H.264 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.261, B:H.264 Salt bridges: B:H.264

18 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.4: 18 residues within 4Å: Chain A: S.8, A.10, P.11, I.14, M.16, F.35, H.37, H.40, I.44, D.46, C.47, C.50, H.51, P.56, V.57, S.58, C.59 Ligands: HEM.6 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:A.10, A:I.14, A:F.35, A:H.40, A:I.44 Hydrogen bonds: A:S.58, A:C.59 Water bridges: A:F.17, A:F.17, A:P.56 Metal complexes: A:H.37, A:H.51 HEM.5: 23 residues within 4Å: Chain A: C.50, H.51, H.52, T.53, D.55, V.57, S.58, C.59, T.61, C.62, H.63, E.70, G.71, D.72, I.74, R.78, A.79, M.80, I.85, R.88, P.94, T.95, S.96 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:T.53, A:V.57, A:D.72, A:I.74, A:A.79, A:I.85, A:P.94, A:P.94 Water bridges: A:A.86, A:R.88, A:R.88 Salt bridges: A:R.78, A:R.88, A:R.88 Metal complexes: A:H.52, A:H.63 HEM.6: 23 residues within 4Å: Chain A: M.16, V.33, F.35, N.36, I.39, H.40, K.43, I.44, T.49, C.50, T.95, S.96, C.97, C.100, H.101, E.104, T.129, C.130, K.212, L.213, A.216 Ligands: HEM.4, HEM.8 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:V.33, A:F.35, A:I.39, A:K.43, A:I.44, A:T.49, A:L.213, A:L.213, A:A.216 Hydrogen bonds: A:K.212 Water bridges: A:N.36, A:D.211, A:K.212 Salt bridges: A:H.40, A:K.43, A:K.212 Metal complexes: A:H.40, A:H.101 HEM.7: 22 residues within 4Å: Chain A: Q.102, T.105, R.108, E.110, C.111, C.114, H.115, T.118, T.119, P.120, K.121, W.126, L.204, I.208, D.211, L.213, A.214, F.217, H.218, I.223, L.224, T.227 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:T.105, A:I.208, A:I.208, A:D.211, A:L.213, A:A.214, A:F.217, A:F.217, A:I.223, A:T.227 Hydrogen bonds: A:Q.102, A:T.118, A:K.121 Water bridges: A:Q.102, A:H.115 Salt bridges: A:H.115 Metal complexes: A:H.115, A:H.218 HEM.8: 26 residues within 4Å: Chain A: M.16, F.17, P.18, A.29, M.30, K.31, P.32, V.33, L.76, M.80, H.81, C.97, H.101, D.122, W.126, C.127, C.130, H.131 Chain B: R.231, S.232, P.239, S.243, C.244 Ligands: ACT.3, HEM.6, ACT.13 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:M.16, A:P.18, A:V.33, A:L.76, A:M.80, A:W.126, A:W.126, A:W.126 Hydrogen bonds: A:F.17, A:M.30, A:M.30, A:V.33, B:S.243 Salt bridges: A:H.131 Metal complexes: A:H.81, A:H.131 HEM.9: 21 residues within 4Å: Chain A: V.172, A.177, P.178, V.181, I.183, F.195, H.197, L.201, L.224, C.225, C.228, H.229, S.235, L.236, P.238, K.240, C.241, Y.263 Chain B: K.26, A.28 Ligands: HEM.11 15 PLIP interactions: 3 interactions with chain B, 12 interactions with chain A, Hydrophobic interactions: B:A.28, A:V.172, A:A.177, A:P.178, A:I.183, A:L.201, A:L.236, A:P.238 Water bridges: B:K.26, A:G.242 Salt bridges: B:K.26, A:K.240 Hydrogen bonds: A:C.241 Metal complexes: A:H.197, A:H.229 HEM.10: 16 residues within 4Å: Chain A: C.228, H.229, H.230, R.231, P.239, K.240, C.241, C.244, H.245, G.255, R.256, P.257, A.262, L.265, E.266 Ligands: HEM.19 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:P.239, A:R.256, A:P.257, A:A.262, A:L.265, A:E.266 Water bridges: A:I.117, A:H.230, A:R.231 Salt bridges: A:H.230, A:R.231, A:R.231 pi-Stacking: A:H.230 Metal complexes: A:H.230, A:H.245 HEM.11: 23 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, C.228, E.266, C.267, C.270, H.271, M.274, V.276, R.278, P.279, T.286, C.287 Ligands: HEM.9, HEM.12 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:I.117, A:I.183, A:L.204, A:V.276, A:V.276, A:P.279, A:T.286 Hydrogen bonds: A:S.203 Water bridges: A:T.196, A:T.196, A:H.200 Salt bridges: A:R.199, A:H.200 Metal complexes: A:H.200, A:H.271 HEM.12: 22 residues within 4Å: Chain A: I.183, D.184, A.185, L.186, A.187, D.188, K.189, Y.190, S.193, M.260, Y.263, H.264, C.267, M.268, H.271, R.280, D.281, D.283, C.284, C.287, H.288 Ligands: HEM.11 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:I.183, A:L.186, A:Y.190, A:Y.263, A:Y.263 Hydrogen bonds: A:L.186, A:D.188, A:K.189, A:Y.190 Water bridges: A:Y.190 Metal complexes: A:H.264, A:H.288 HEM.15: 17 residues within 4Å: Chain B: S.8, A.10, P.11, I.14, M.16, F.35, H.37, H.40, I.44, D.46, C.47, C.50, H.51, P.56, S.58, C.59 Ligands: HEM.17 11 PLIP interactions: 11 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:S.58, B:C.59 Water bridges: B:S.60 Metal complexes: B:H.37, B:H.51 HEM.16: 21 residues within 4Å: Chain B: C.50, H.52, T.53, V.57, S.58, C.59, T.61, C.62, H.63, E.70, G.71, D.72, I.74, R.78, A.79, M.80, I.85, R.88, P.94, T.95, S.96 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:T.53, B:V.57, B:D.72, B:I.74, B:A.79, B:P.94, B:P.94 Hydrogen bonds: B:D.72 Water bridges: B:R.78, B:R.78, B:A.86, B:R.88 Salt bridges: B:R.78, B:R.88, B:R.88 Metal complexes: B:H.52, B:H.63 HEM.17: 23 residues within 4Å: Chain B: M.16, V.33, F.35, N.36, I.39, H.40, K.43, I.44, T.49, C.50, T.95, S.96, C.97, C.100, H.101, E.104, T.129, C.130, K.212, L.213, A.216 Ligands: HEM.15, HEM.19 21 PLIP interactions: 21 interactions with chain B, Hydrophobic interactions: B:V.33, B:F.35, B:F.35, B:I.39, B:K.43, B:I.44, B:T.49, B:L.213, B:L.213, B:A.216 Hydrogen bonds: B:K.212 Water bridges: B:N.36, B:N.36, B:N.36, B:K.212 Salt bridges: B:H.40, B:K.43, B:K.212 pi-Stacking: B:F.35 Metal complexes: B:H.40, B:H.101 HEM.18: 21 residues within 4Å: Chain B: Q.102, T.105, R.108, E.110, C.111, C.114, H.115, T.118, T.119, P.120, K.121, W.126, I.208, D.211, L.213, A.214, F.217, H.218, I.223, L.224, T.227 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:T.105, B:T.118, B:I.208, B:I.208, B:D.211, B:L.213, B:A.214, B:F.217, B:F.217, B:I.223, B:L.224 Hydrogen bonds: B:Q.102, B:T.118, B:K.121 Water bridges: B:H.115 Salt bridges: B:H.115 Metal complexes: B:H.115, B:H.218 HEM.19: 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, V.33, L.76, M.80, H.81, C.97, H.101, D.122, W.126, C.127, C.130, H.131 Ligands: ACT.2, HEM.10, HEM.17 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A, Hydrophobic interactions: B:M.16, B:P.18, B:V.33, B:M.80, B:W.126, B:W.126, A:P.239 Hydrogen bonds: B:F.17, B:M.30, B:M.30, B:V.33, A:S.243 Salt bridges: B:H.131 Metal complexes: B:H.81, B:H.131 HEM.20: 20 residues within 4Å: Chain A: K.26 Chain B: V.172, A.177, P.178, V.181, I.183, F.195, H.197, L.201, L.224, C.225, C.228, H.229, S.235, L.236, P.238, K.240, C.241, Y.263 Ligands: HEM.22 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:V.172, B:A.177, B:P.178, B:V.181, B:V.181, B:I.183, B:F.195, B:L.201, B:L.201, B:L.236 Hydrogen bonds: B:C.241 Salt bridges: B:K.240 Metal complexes: B:H.197, B:H.229 Water bridges: A:K.26 HEM.21: 16 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, G.255, R.256, P.257, A.262, L.265, E.266 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:P.239, B:R.256, B:P.257, B:A.262, B:L.265 Water bridges: B:I.117, B:H.230, B:R.231 Salt bridges: B:H.230, B:R.231, B:R.231 Metal complexes: B:H.230, B:H.245 HEM.22: 20 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, E.266, C.267, C.270, H.271, M.274, V.276, P.279, T.286 Ligands: HEM.20, HEM.23 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:I.117, B:I.183, B:L.204, B:V.276, B:P.279 Hydrogen bonds: B:T.196, B:S.203 Water bridges: B:T.196 Salt bridges: B:R.199, B:H.200 Metal complexes: B:H.200, B:H.271 HEM.23: 22 residues within 4Å: Chain B: I.183, D.184, A.185, L.186, A.187, D.188, K.189, Y.190, S.193, M.260, Y.263, H.264, C.267, M.268, H.271, R.280, D.281, D.283, C.284, C.287, H.288 Ligands: HEM.22 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:I.183, B:L.186, B:K.189, B:Y.190, B:Y.190, B:Y.263, B:Y.263 Hydrogen bonds: B:L.186, B:D.188, B:K.189, B:Y.190 Water bridges: B:Y.190 Metal complexes: B:H.264, B:H.288

Links

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Citation

Matias, P.M. et al., The primary and three-dimensional structures of a nine-haem cytochrome c from Desulfovibrio desulfuricans ATCC 27774 reveal a new member of the Hmc family. Structure Fold.Des. (1999)

Release Date

1999-12-01

Peptides

PROTEIN (NINE-HAEM CYTOCHROME C): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PROTEIN (NINE-HAEM CYTOCHROME C)