SMTL ID : 1h29.2 (3 other biounits)

Sulfate respiration in Desulfovibrio vulgaris Hildenborough: Structure of the 16-heme Cytochrome c HmcA at 2.5 A resolution and a view of its role in transmembrane electron transfer

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.51 Å

Oligo State

monomer

Ligands

16 x HEC: HEME C(Covalent)

HEC.1: 23 residues within 4Å: Chain A: I.15, I.17, F.33, H.35, H.38, T.39, V.42, D.48, C.49, C.52, H.53, M.60, L.62, K.63, F.64, R.66, Y.79, H.191, I.195, M.199, V.211 Ligands: HEC.2, HEC.7 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:I.15, A:I.15, A:I.17, A:F.33, A:T.39, A:V.42, A:L.62, A:F.64, A:H.191, A:I.195, A:I.195 Hydrogen bonds: A:F.64 Salt bridges: A:R.66, A:H.191 pi-Stacking: A:H.35, A:H.53 Metal complexes: A:H.35, A:H.53 HEC.2: 24 residues within 4Å: Chain A: I.17, V.31, A.32, F.33, R.34, Q.37, H.38, A.41, V.42, M.45, C.52, F.64, Y.79, N.82, C.83, C.86, H.87, L.90, K.96, T.97, G.98, P.99, S.106 Ligands: HEC.1 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:V.31, A:F.33, A:Q.37, A:A.41, A:V.42, A:F.64, A:F.64, A:Y.79 Hydrogen bonds: A:Q.37, A:Q.37 Salt bridges: A:R.34, A:K.96 pi-Stacking: A:F.33 Metal complexes: A:H.38, A:H.87 HEC.3: 20 residues within 4Å: Chain A: I.17, G.18, A.19, M.20, L.26, D.27, L.28, V.31, K.76, Y.79, H.80, C.83, I.84, H.87, Q.100, D.101, E.103, C.104, C.107, H.108 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:I.17, A:L.28, A:V.31, A:K.76, A:K.76, A:Y.79, A:Y.79, A:Y.79, A:I.84, A:I.84 Hydrogen bonds: A:M.20, A:D.27, A:L.28 Water bridges: A:K.25, A:D.27 Metal complexes: A:H.80, A:H.108 HEC.4: 25 residues within 4Å: Chain A: G.122, F.123, H.128, H.131, V.132, I.137, K.145, N.146, C.147, C.150, H.151, E.168, D.169, S.170, C.171, R.172, L.234, D.235, D.276, C.277, R.278, I.285 Ligands: HEC.5, HEC.6, HEC.8 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:F.123, A:F.123, A:H.131, A:V.132, A:I.137, A:K.145, A:E.168, A:L.234, A:L.234, A:I.285 Hydrogen bonds: A:F.123, A:S.170, A:C.277, A:R.278 Salt bridges: A:R.172, A:R.278, A:R.278 Metal complexes: A:H.128, A:H.151 HEC.5: 16 residues within 4Å: Chain A: C.150, H.151, H.152, Y.154, L.161, D.169, S.170, C.171, C.174, H.175, K.182, R.183, P.184, A.189, T.192 Ligands: HEC.4 10 PLIP interactions: 10 interactions with chain A, Hydrophobic interactions: A:Y.154, A:L.161, A:D.169, A:R.183, A:P.184, A:A.189 Salt bridges: A:K.59 pi-Stacking: A:H.152 Metal complexes: A:H.152, A:H.175 HEC.6: 22 residues within 4Å: Chain A: I.121, F.123, L.127, R.130, H.131, S.134, A.136, I.137, C.150, A.193, C.194, C.197, H.198, V.201, E.207, T.208, G.209, P.210, F.225, K.226 Ligands: HEC.4, HEC.7 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:I.121, A:F.123, A:L.127, A:L.127, A:A.136, A:I.137, A:I.137, A:I.137, A:V.201, A:F.225, A:F.225 Hydrogen bonds: A:K.226 Water bridges: A:R.130, A:R.130, A:R.130 Salt bridges: A:R.130, A:R.130 pi-Stacking: A:F.123 Metal complexes: A:H.131, A:H.198 HEC.7: 20 residues within 4Å: Chain A: I.15, H.35, W.118, E.120, I.121, L.186, D.187, A.190, H.191, C.194, I.195, H.198, P.210, V.211, N.212, C.213, C.216, H.217 Ligands: HEC.1, HEC.6 10 PLIP interactions: 10 interactions with chain A, Hydrophobic interactions: A:I.15, A:I.121, A:L.186, A:A.190, A:I.195 Hydrogen bonds: A:I.121 pi-Stacking: A:W.118, A:W.118 Metal complexes: A:H.191, A:H.217 HEC.8: 22 residues within 4Å: Chain A: L.234, Q.238, P.239, A.242, L.243, I.244, F.265, H.267, E.271, A.274, D.276, C.277, C.280, H.281, I.285, D.286, T.287, C.288, T.289, R.375 Ligands: HEC.4, HEC.10 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:Q.238, A:P.239, A:A.242, A:I.244, A:I.244, A:F.265, A:F.265, A:A.274, A:I.285, A:I.285, A:T.287 Hydrogen bonds: A:C.288, A:T.289 Water bridges: A:R.375 Salt bridges: A:R.375 Metal complexes: A:H.267, A:H.281 HEC.9: 17 residues within 4Å: Chain A: C.280, H.281, H.282, V.283, R.284, T.287, C.288, C.291, H.292, D.299, S.300, K.301, K.307, A.308, Q.311, S.314, R.316 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:V.283, A:A.308 Hydrogen bonds: A:S.314, A:S.314 Salt bridges: A:H.282, A:R.316 pi-Cation interactions: A:R.316 Metal complexes: A:H.282, A:H.292 HEC.10: 24 residues within 4Å: Chain A: I.244, V.263, F.265, D.266, H.270, K.273, T.279, C.280, M.315, R.316, S.317, C.318, C.321, H.322, R.325, C.350, R.386, D.432, K.433, L.434, T.437, F.438 Ligands: HEC.8, HEC.12 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:I.244, A:V.263, A:F.265, A:F.265, A:K.273, A:T.279, A:L.434, A:L.434, A:F.438 Hydrogen bonds: A:R.325, A:D.432, A:K.433, A:L.434 Salt bridges: A:H.270, A:R.386 pi-Stacking: A:F.438 Metal complexes: A:H.270, A:H.322 HEC.11: 21 residues within 4Å: Chain A: V.326, Q.328, T.330, C.331, C.334, H.335, I.338, P.340, T.341, K.342, Q.346, I.429, D.432, L.434, A.435, F.438, H.439, T.444, L.445, Q.447, G.448 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:V.326, A:T.330, A:I.338, A:I.429, A:D.432, A:L.434, A:A.435, A:F.438, A:F.438, A:T.444, A:L.445, A:L.445, A:Q.447 Hydrogen bonds: A:T.341, A:T.341, A:K.342 Water bridges: A:S.343 Salt bridges: A:H.335 Metal complexes: A:H.335, A:H.439 HEC.12: 17 residues within 4Å: Chain A: I.244, L.245, P.246, T.259, M.260, K.261, P.262, V.263, L.305, M.309, H.310, C.318, Q.346, C.347, C.350, H.351 Ligands: HEC.10 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:I.244, A:I.244, A:P.246, A:V.263, A:V.263, A:L.305, A:M.309 Hydrogen bonds: A:L.245, A:M.260, A:M.260 Salt bridges: A:H.351 Metal complexes: A:H.310, A:H.351 HEC.13: 22 residues within 4Å: Chain A: T.392, I.398, P.399, V.402, I.404, F.416, H.418, I.421, V.422, L.425, L.445, C.446, C.449, H.450, S.456, L.457, P.459, K.461, C.462, Y.484, Q.487 Ligands: HEC.15 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:T.392, A:I.398, A:P.399, A:V.402, A:V.402, A:I.404, A:I.421, A:V.422, A:L.425, A:P.459 Hydrogen bonds: A:C.462, A:Y.484 Water bridges: A:P.459, A:K.461 Salt bridges: A:K.461, A:K.461 Metal complexes: A:H.418, A:H.450 HEC.14: 18 residues within 4Å: Chain A: F.337, K.339, C.449, H.450, H.451, N.452, P.460, K.461, C.462, S.464, C.465, H.466, D.476, R.477, P.478, A.483, Q.486, Q.487 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:F.337, A:N.452, A:P.460, A:R.477, A:A.483, A:Q.486, A:Q.487 Hydrogen bonds: A:N.452, A:Q.486 Water bridges: A:K.339 Salt bridges: A:K.339, A:H.451 pi-Stacking: A:F.337 Metal complexes: A:H.451, A:H.466 HEC.15: 18 residues within 4Å: Chain A: G.333, I.404, S.414, F.416, P.417, I.421, T.424, C.449, Q.487, C.488, C.491, H.492, M.495, K.499, P.500, C.508 Ligands: HEC.13, HEC.16 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:I.404, A:F.416, A:F.416, A:P.417, A:I.421, A:T.424, A:Q.487, A:K.499, A:K.499, A:P.500 Salt bridges: A:K.420, A:K.420, A:K.499 pi-Stacking: A:F.416 Metal complexes: A:H.492 HEC.16: 22 residues within 4Å: Chain A: I.404, G.405, S.406, I.407, A.408, K.409, E.410, Y.411, S.414, K.481, Y.484, H.485, C.488, H.492, A.501, N.502, T.503, A.504, C.505, C.508, H.509 Ligands: HEC.15 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:I.407, A:Y.411, A:K.481, A:Y.484 Hydrogen bonds: A:I.407, A:K.409, A:E.410, A:Y.411 pi-Stacking: A:H.509 pi-Cation interactions: A:K.481 Metal complexes: A:H.485, A:H.509

Links

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Citation

Matias, P.M. et al., Sulfate Respiration in Desulfovibrio Vulgaris Hildenborough: Structure of the 16-Heme Cytochrome C Hmca at 2.5 A Resolution and a View of its Role in Transmembrane Electron Transfer. J.Biol.Chem. (2002)

Release Date

2002-10-02

Peptides

HIGH-MOLECULAR-WEIGHT CYTOCHROME C: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

HIGH-MOLECULAR-WEIGHT CYTOCHROME C

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