SMTL ID : 2cvc.1

Crystal structure of High-Molecular Weight Cytochrome c from Desulfovibrio vulgaris (Hildenborough)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

16 x HEC: HEME C(Covalent)

HEC.1: 22 residues within 4Å: Chain A: I.46, I.48, F.64, H.66, H.69, T.70, V.73, C.80, C.83, H.84, M.91, L.93, K.94, F.95, R.97, Y.110, H.222, I.226, M.230, V.242 Ligands: HEC.2, HEC.7 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:I.48, A:H.69, A:T.70, A:V.73, A:L.93, A:H.222, A:I.226, A:I.226, A:V.242 Hydrogen bonds: A:F.95, A:Y.110 Water bridges: A:L.93, A:R.97, A:R.97 Salt bridges: A:R.97, A:H.222 pi-Stacking: A:H.66 Metal complexes: A:H.66, A:H.84 HEC.2: 21 residues within 4Å: Chain A: I.48, V.62, F.64, R.65, Q.68, H.69, A.72, V.73, C.83, F.95, N.113, C.114, C.117, H.118, L.121, K.127, T.128, G.129, P.130 Ligands: HEC.1, HEC.3 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:I.48, A:V.62, A:F.64, A:Q.68, A:A.72, A:V.73, A:F.95, A:P.130 Hydrogen bonds: A:Q.68 Water bridges: A:R.65, A:R.65, A:K.127 Salt bridges: A:R.65, A:K.127 pi-Stacking: A:H.69 pi-Cation interactions: A:H.69, A:H.118 Metal complexes: A:H.69, A:H.118 HEC.3: 21 residues within 4Å: Chain A: I.48, G.49, A.50, M.51, L.57, D.58, L.59, V.62, K.107, Y.110, H.111, C.114, I.115, H.118, Q.131, D.132, E.134, C.135, C.138, H.139 Ligands: HEC.2 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:I.48, A:L.57, A:K.107, A:Y.110, A:Y.110, A:Y.110, A:I.115, A:I.115 Hydrogen bonds: A:A.50, A:M.51, A:D.58, A:L.59 Metal complexes: A:H.111, A:H.139 HEC.4: 24 residues within 4Å: Chain A: G.153, F.154, H.159, H.162, V.163, I.168, N.177, C.178, C.181, H.182, E.199, D.200, S.201, C.202, R.203, L.265, D.266, D.307, C.308, R.309, I.316 Ligands: HEC.5, HEC.6, HEC.8 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:F.154, A:F.154, A:H.162, A:V.163, A:I.168, A:E.199, A:L.265, A:L.265, A:I.316 Hydrogen bonds: A:F.154, A:C.308, A:R.309 Water bridges: A:R.309 Salt bridges: A:R.203, A:R.309, A:R.309 pi-Stacking: A:H.159 Metal complexes: A:H.159, A:H.182 HEC.5: 17 residues within 4Å: Chain A: K.90, C.181, H.183, Y.185, L.192, D.200, S.201, C.202, C.205, H.206, K.213, R.214, P.215, A.220, T.223, A.224 Ligands: HEC.4 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:Y.185, A:L.192, A:L.192, A:D.200, A:R.214, A:P.215, A:A.220, A:T.223, A:A.224 Salt bridges: A:K.90, A:K.213 Metal complexes: A:H.183, A:H.206 HEC.6: 21 residues within 4Å: Chain A: I.152, F.154, L.158, R.161, H.162, S.165, A.167, I.168, C.181, A.224, C.225, C.228, H.229, E.238, T.239, G.240, P.241, F.256, K.257 Ligands: HEC.4, HEC.7 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:I.152, A:F.154, A:F.154, A:L.158, A:A.167, A:I.168, A:F.256, A:F.256 Hydrogen bonds: A:K.257 Water bridges: A:R.161, A:R.161, A:R.161, A:R.161, A:R.161, A:R.161 Salt bridges: A:R.161, A:R.161 Metal complexes: A:H.162, A:H.229 HEC.7: 21 residues within 4Å: Chain A: I.46, H.66, W.149, E.151, I.152, R.203, L.217, D.218, A.221, H.222, C.225, I.226, H.229, P.241, V.242, N.243, C.244, C.247, H.248 Ligands: HEC.1, HEC.6 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: A:I.46, A:W.149, A:L.217, A:L.217, A:A.221, A:I.226 Hydrogen bonds: A:I.152 Water bridges: A:E.151 Salt bridges: A:R.203 Metal complexes: A:H.222, A:H.248 HEC.8: 21 residues within 4Å: Chain A: L.265, R.267, Q.269, P.270, I.275, F.296, H.298, H.301, E.302, A.305, D.307, C.308, C.311, H.312, I.316, D.317, T.318, C.319, T.320 Ligands: HEC.4, HEC.10 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:Q.269, A:I.275, A:F.296, A:H.301, A:A.305, A:I.316 Hydrogen bonds: A:C.319, A:T.320 Water bridges: A:L.274, A:L.276, A:T.320 Metal complexes: A:H.298, A:H.312 HEC.9: 19 residues within 4Å: Chain A: C.311, H.312, H.313, V.314, R.315, T.318, C.319, C.322, H.323, D.330, S.331, K.332, V.334, K.338, A.339, Q.342, S.345, R.347, S.348 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:V.314, A:V.314, A:K.332, A:V.334, A:A.339 Hydrogen bonds: A:Q.342, A:S.345 Water bridges: A:H.313, A:R.347 Salt bridges: A:H.313, A:R.347 pi-Cation interactions: A:R.347 Metal complexes: A:H.313, A:H.323 HEC.10: 23 residues within 4Å: Chain A: I.275, F.296, D.297, A.300, H.301, K.304, T.310, C.311, M.346, R.347, S.348, C.349, C.352, H.353, R.356, C.381, R.417, K.464, L.465, T.468, F.469 Ligands: HEC.8, HEC.12 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:I.275, A:K.304, A:T.310, A:L.465, A:F.469 Water bridges: A:R.417, A:R.417, A:K.464 Salt bridges: A:H.301, A:H.301, A:R.417 pi-Stacking: A:H.353, A:F.469 Metal complexes: A:H.301, A:H.353 HEC.11: 20 residues within 4Å: Chain A: V.357, T.361, C.362, C.365, H.366, I.369, P.371, T.372, Q.377, L.456, I.460, D.463, L.465, A.466, F.469, H.470, T.475, L.476, Q.478, G.479 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:V.357, A:I.369, A:L.456, A:I.460, A:D.463, A:L.465, A:A.466, A:F.469, A:F.469, A:T.475, A:Q.478 Hydrogen bonds: A:T.372, A:Q.377 Water bridges: A:K.373 Salt bridges: A:H.366 pi-Stacking: A:H.366 Metal complexes: A:H.366, A:H.470 HEC.12: 21 residues within 4Å: Chain A: I.275, L.276, P.277, G.289, T.290, M.291, K.292, P.293, V.294, L.336, E.337, M.340, H.341, C.349, K.373, Q.377, C.378, C.381, H.382, F.469 Ligands: HEC.10 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:I.275, A:I.275, A:P.277, A:V.294, A:L.336, A:M.340, A:K.373, A:F.469, A:F.469 Hydrogen bonds: A:L.276, A:T.290, A:M.291, A:V.294 Water bridges: A:M.291 Salt bridges: A:H.382 pi-Stacking: A:H.341, A:H.382 Metal complexes: A:H.341, A:H.382 HEC.13: 17 residues within 4Å: Chain A: I.429, I.435, F.447, H.449, V.453, L.456, L.476, C.477, C.480, H.481, S.487, L.488, P.490, K.492, C.493, Y.515 Ligands: HEC.15 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:I.429, A:I.435, A:F.447, A:V.453, A:L.456, A:P.490 Hydrogen bonds: A:C.493, A:Y.515 Water bridges: A:G.436, A:S.437, A:A.494 Salt bridges: A:K.492 Metal complexes: A:H.449, A:H.481 HEC.14: 16 residues within 4Å: Chain A: F.368, C.480, H.482, N.483, P.491, K.492, C.493, S.495, C.496, H.497, D.507, R.508, P.509, A.514, Q.517, Q.518 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:F.368, A:N.483, A:P.491, A:R.508, A:P.509, A:A.514, A:Q.517, A:Q.518 Hydrogen bonds: A:N.483, A:Q.517 Water bridges: A:D.507 pi-Stacking: A:F.368, A:H.497 Metal complexes: A:H.482, A:H.497 HEC.15: 21 residues within 4Å: Chain A: G.364, I.435, S.445, F.447, P.448, K.451, I.452, T.455, C.480, Q.518, C.519, C.522, H.523, M.526, I.528, K.530, P.531, D.538, C.539 Ligands: HEC.13, HEC.16 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: A:I.435, A:F.447, A:F.447, A:I.452, A:Q.518, A:I.528, A:P.531 Hydrogen bonds: A:T.455 Salt bridges: A:K.451, A:K.451 Metal complexes: A:H.523 HEC.16: 20 residues within 4Å: Chain A: I.435, G.436, S.437, I.438, A.439, K.440, E.441, Y.442, K.512, Y.515, H.516, C.519, M.520, H.523, A.532, N.533, C.536, C.539, H.540 Ligands: HEC.15 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:I.435, A:Y.442, A:K.512, A:Y.515, A:Y.515 Hydrogen bonds: A:I.438, A:K.440, A:E.441, A:Y.442, A:Y.442 Water bridges: A:S.437, A:S.437 pi-Stacking: A:H.516, A:H.540 Metal complexes: A:H.516, A:H.540

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Suto, K. et al., Structure of High-Molecular Weight Cytochrome c. To be Published

Release Date

2006-06-06

Peptides

High-molecular-weight cytochrome c precursor: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

High-molecular-weight cytochrome c precursor

Related Entries With Identical Sequence