SMTL ID : 1ofw.1 (1 other biounit)

Three dimensional structure of the oxidized form of nine heme cytochrome c at PH 7.5

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

9 x HEC: HEME C(Covalent)

HEC.1: 17 residues within 4Å: Chain A: S.8, A.10, I.14, M.16, F.35, H.37, H.40, I.44, N.46, C.47, C.50, H.51, P.56, V.57, S.58, C.59 Ligands: HEC.3 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: A:A.10, A:F.35, A:H.40, A:I.44, A:P.56 Hydrogen bonds: A:S.58, A:C.59 Water bridges: A:P.56, A:S.60 Metal complexes: A:H.37, A:H.51 HEC.2: 21 residues within 4Å: Chain A: C.50, H.52, T.53, D.55, V.57, S.58, C.59, T.61, C.62, H.63, E.70, G.71, N.72, R.78, A.79, M.80, I.85, R.88, P.94, V.95, S.96 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:V.57, A:A.79, A:I.85, 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.52 Metal complexes: A:H.52, A:H.63 HEC.3: 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, V.95, S.96, C.97, C.100, H.101, Q.104, T.129, C.130, K.212, L.213, A.216 Ligands: HEC.1, HEC.5 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:V.33, A:F.35, A:I.39, A:I.44, A:T.49, A:V.95, A:L.213, A:L.213, A:A.216 Hydrogen bonds: A:K.212 Water bridges: A:N.36, A:Q.166, A:Q.166, A:Q.166, A:K.212 Salt bridges: A:K.43, A:K.212 pi-Stacking: A:F.35 Metal complexes: A:H.40, A:H.101 HEC.4: 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, I.223, L.224, T.227 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:T.105, A:V.118, A:V.118, A:L.204, A:I.208, A:D.211, A:L.213, A:A.214, A:F.217, A:F.217, A:I.223, A:L.224, A:T.227 Hydrogen bonds: A:K.121, A:R.122 Water bridges: A:K.121, A:R.122, A:D.123 Salt bridges: A:K.121, A:R.122 Metal complexes: A:H.115, A:H.218 HEC.5: 19 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, R.122, W.126, C.127, C.130, H.131 Ligands: HEC.3 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:M.16, A:P.18, A:V.33, A:M.80, A:W.126, A:W.126 Hydrogen bonds: A:F.17, A:M.30, A:M.30, A:V.33 Salt bridges: A:H.131 Metal complexes: A:H.81, A:H.131 HEC.6: 19 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 Ligands: HEC.8 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:V.172, A:A.177, A:P.178, A:V.181, A:I.183, A:F.195, A:L.201, A:L.201, A:L.236, A:P.238 Hydrogen bonds: A:C.241, A:Y.263 Water bridges: A:K.240, A:G.242 Salt bridges: A:K.240 Metal complexes: A:H.197, A:H.229 HEC.7: 15 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, Q.266 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:P.239, A:R.256, A:P.257, A:A.262, A:L.265, A:Q.266 Water bridges: A:I.117, A:I.117, A:T.119, A:H.230, A:R.231, A:G.255 Salt bridges: A:H.230, A:R.231, A:R.231 pi-Cation interactions: A:R.231 Metal complexes: A:H.230, A:H.245 HEC.8: 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, R.207, Q.266, C.267, C.270, H.271, M.274, V.276, R.278, P.279, T.286, C.287 Ligands: HEC.6, HEC.9 20 PLIP interactions: 20 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:T.196, A:S.203 Water bridges: A:N.194, A:T.196 Salt bridges: A:R.199, A:H.200, A:R.207 pi-Stacking: A:H.200, A:H.200, A:H.271, A:H.271 Metal complexes: A:H.200, A:H.271 HEC.9: 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: HEC.8 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:I.183, A:L.186, A:K.189, 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:D.188, A:Y.190 Metal complexes: A:H.264, A:H.288

1 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.137, M.142 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.27, A:A.29 Water bridges: A:A.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bento, I. et al., Redox-Bohr and Other Cooperativity Effects in the Nine-Heme Cytochrome C from Desulfovibrio Desulfuricans Atcc 27774: Crystallographic and Modeling Studies. J.Biol.Chem. (2003)

Release Date

2003-09-18

Peptides

NINE-HEME CYTOCHROME C: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

NINE-HEME CYTOCHROME C

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