SMTL ID : 1z1n.1

Crystal Structure of the sixteen heme cytochrome from Desulfovibrio gigas

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x NAG- NAA: 2-acetamido-2-deoxy-beta-D-allopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAA.1: 2 residues within 4Å: Chain A: T.288, N.290 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.290

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 1 residues within 4Å: Chain A: H.483 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.483, H2O.6, H2O.6, H2O.13, H2O.14 ZN.3: 2 residues within 4Å: Chain A: E.416, E.419 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.416, A:E.419, H2O.16, H2O.16, H2O.16 ZN.4: 5 residues within 4Å: Chain A: M.450, D.455, W.457, Q.458 Ligands: HEC.20 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:W.457, H2O.6, H2O.16, H2O.16

16 x HEC: HEME C(Non-covalent)(Covalent)

HEC.5: 22 residues within 4Å: Chain A: I.45, I.47, T.49, F.63, H.65, H.68, T.69, L.72, C.79, C.82, H.83, F.92, K.93, F.94, R.96, Y.110, R.225, H.229, V.249, L.250 Ligands: HEC.6, HEC.11 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:I.45, A:I.47, A:F.63, A:F.63, A:H.68, A:L.72, A:F.92, A:F.92, A:F.92, A:F.94, A:H.229, A:L.250 Hydrogen bonds: A:F.94 Water bridges: A:D.226 Salt bridges: A:R.96, A:R.225, A:H.229 Metal complexes: A:H.65, A:H.83 HEC.6: 19 residues within 4Å: Chain A: I.47, F.63, K.67, H.68, A.71, L.72, S.81, C.82, F.94, N.113, C.114, C.117, H.118, Y.125, P.129, R.136, C.137 Ligands: HEC.5, HEC.7 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:I.47, A:K.67, A:A.71, A:L.72, A:L.72, A:F.94, A:F.94, A:Y.125, A:Y.125, A:P.129 Salt bridges: A:K.67, A:R.136 pi-Stacking: A:F.63 Metal complexes: A:H.68, A:H.118 HEC.7: 21 residues within 4Å: Chain A: I.47, D.48, T.49, A.50, L.56, E.57, Q.58, V.61, K.103, A.107, Y.110, H.111, C.114, M.115, A.131, A.132, E.133, C.134, C.137, H.138 Ligands: HEC.6 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:L.56, A:E.57, A:Q.58, A:V.61, A:A.107, A:Y.110, A:Y.110, A:Y.110 Hydrogen bonds: A:T.49, A:A.50, A:E.57, A:Q.58 Water bridges: A:Q.58 Salt bridges: A:K.103 Metal complexes: A:H.111, A:H.138 HEC.8: 22 residues within 4Å: Chain A: S.153, L.154, H.159, H.162, V.163, E.166, E.174, S.177, C.178, C.181, H.182, E.199, G.200, S.201, C.202, L.272, R.274, N.318, C.319, V.320 Ligands: HEC.9, HEC.10 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:L.154, A:L.154, A:H.162, A:V.163, A:V.163, A:E.166, A:E.199, A:E.199, A:L.272, A:L.272, A:R.274 Hydrogen bonds: A:L.154, A:L.154, A:C.319, A:V.320 Water bridges: A:S.153, A:L.154 Metal complexes: A:H.159, A:H.182 HEC.9: 17 residues within 4Å: Chain A: C.181, H.182, H.183, T.184, Y.185, L.192, C.202, C.205, H.206, S.213, R.219, V.220, V.221, A.227, E.230, S.231 Ligands: HEC.8 10 PLIP interactions: 10 interactions with chain A, Hydrophobic interactions: A:Y.185, A:L.192, A:L.192, A:A.227, A:E.230 Hydrogen bonds: A:S.213 Salt bridges: A:K.89, A:R.219 Metal complexes: A:H.183, A:H.206 HEC.10: 18 residues within 4Å: Chain A: L.154, L.158, R.161, H.162, A.165, C.181, S.231, C.232, C.235, H.236, E.245, S.246, G.247, P.248, W.263, K.264 Ligands: HEC.8, HEC.11 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:L.154, A:L.158, A:W.263 Hydrogen bonds: A:K.264 Water bridges: A:A.165 Salt bridges: A:R.161, A:R.161 Metal complexes: A:H.162, A:H.236 HEC.11: 24 residues within 4Å: Chain A: V.42, D.43, I.45, H.65, E.144, A.146, T.147, K.151, P.152, T.224, R.225, S.228, H.229, C.232, V.233, H.236, P.248, V.249, L.250, C.251, C.254, H.255 Ligands: HEC.5, HEC.10 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:I.45, A:E.144, A:A.146, A:K.151, A:P.152, A:T.224, A:R.225, A:V.233 Water bridges: A:K.151, A:K.151, A:K.151, A:K.151 Salt bridges: A:K.151 Metal complexes: A:H.229, A:H.255 HEC.12: 25 residues within 4Å: Chain A: L.156, L.272, R.274, G.275, Q.276, P.277, T.280, L.282, F.307, H.309, H.312, E.313, V.316, N.318, C.319, C.322, H.323, L.332, A.334, C.335, K.415, R.418 Ligands: HEC.13, HEC.14, GOL.24 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:L.156, A:R.274, A:T.280, A:L.282, A:F.307, A:F.307, A:H.312, A:E.313, A:V.316, A:V.316 Water bridges: A:K.415, A:K.415, A:E.419 Salt bridges: A:K.415, A:R.418 Metal complexes: A:H.309, A:H.323 HEC.13: 21 residues within 4Å: Chain A: C.322, H.323, H.324, P.325, T.326, Q.327, S.331, A.333, C.335, C.339, H.340, D.347, G.348, N.349, S.356, Q.359, V.362, T.364, S.365 Ligands: HEC.12, GOL.25 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: A:T.326, A:A.333, A:N.349, A:V.362, A:T.364 Hydrogen bonds: A:Q.327, A:T.364 Salt bridges: A:H.324, A:H.324 Metal complexes: A:H.324, A:H.340 HEC.14: 22 residues within 4Å: Chain A: V.305, F.307, D.308, H.312, F.315, V.316, T.321, C.322, T.363, S.365, C.366, C.369, H.370, Q.373, R.377, S.478, P.479, M.480, H.483, F.484 Ligands: HEC.12, HEC.16 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:V.305, A:F.307, A:F.307, A:F.315, A:F.315, A:F.315, A:F.315, A:F.315, A:V.316, A:T.321, A:P.479, A:M.480, A:H.483, A:F.484 Hydrogen bonds: A:M.480 Water bridges: A:R.377, A:R.377, A:R.377 Salt bridges: A:R.377 Metal complexes: A:H.312, A:H.370 HEC.15: 21 residues within 4Å: Chain A: H.370, A.374, E.379, C.380, C.383, H.384, M.387, S.393, N.395, S.396, L.471, A.475, S.478, M.480, A.481, F.484, H.485, T.490, M.491, S.493, G.494 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:H.370, A:A.374, A:E.379, A:L.471, A:A.481, A:F.484, A:F.484, A:M.491 Hydrogen bonds: A:S.393, A:S.396 Water bridges: A:S.393, A:S.393, A:S.393 Metal complexes: A:H.384, A:H.485 HEC.16: 21 residues within 4Å: Chain A: L.282, V.283, A.284, P.302, V.305, T.342, T.353, A.354, A.357, H.358, C.366, H.370, L.392, S.393, S.396, C.397, C.400, H.401, F.484 Ligands: HEC.14, GOL.24 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: A:L.282, A:L.282, A:P.302, A:V.305, A:T.353, A:A.357, A:L.392, A:F.484 Water bridges: A:L.282 Metal complexes: A:H.358, A:H.401 HEC.17: 21 residues within 4Å: Chain A: V.436, N.440, V.441, P.442, L.445, L.447, Y.449, F.462, H.464, I.467, Y.468, L.471, C.492, C.495, H.496, L.503, P.505, K.507, C.508 Ligands: HEC.18, HEC.19 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:V.436, A:V.441, A:P.442, A:L.445, A:L.445, A:L.447, A:F.462, A:F.462, A:I.467, A:Y.468, A:L.471, A:P.505 Hydrogen bonds: A:Y.449, A:C.508 Water bridges: A:A.509 Salt bridges: A:K.507 Metal complexes: A:H.464, A:H.496 HEC.18: 20 residues within 4Å: Chain A: P.386, C.495, H.497, N.498, A.499, P.506, K.507, C.508, S.510, C.511, H.512, T.520, N.522, Q.523, P.524, A.529, N.532, Q.533 Ligands: HEC.17, GOL.23 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:N.498, A:A.499, A:P.506, A:Q.523, A:A.529, A:N.532, A:Q.533 Hydrogen bonds: A:N.498 Water bridges: A:Q.388, A:H.497 Salt bridges: A:H.497, A:H.497 Metal complexes: A:H.497, A:H.512 HEC.19: 21 residues within 4Å: Chain A: C.383, L.447, E.461, F.462, P.463, K.466, I.467, K.470, C.495, F.530, Q.533, C.534, C.537, H.538, M.541, V.543, N.544, P.545, G.552 Ligands: HEC.17, HEC.20 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:L.447, A:F.462, A:F.462, A:I.467, A:K.470, A:F.530, A:Q.533, A:V.543, A:P.545 Water bridges: A:K.466 Salt bridges: A:K.466, A:K.466 Metal complexes: A:H.538 HEC.20: 22 residues within 4Å: Chain A: L.447, N.448, Y.449, M.450, D.455, E.456, W.457, A.460, K.527, F.530, H.531, C.534, I.535, H.538, K.546, A.547, D.549, C.550, C.553, H.554 Ligands: ZN.4, HEC.19 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:L.447, A:A.460, A:F.530, A:F.530, A:I.535 Hydrogen bonds: A:Y.449, A:M.450, A:M.450, A:E.456, A:W.457, A:Q.458 pi-Stacking: A:H.554 pi-Cation interactions: A:K.527 Metal complexes: A:H.531, A:H.554

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.21: 1 residues within 4Å: Chain A: D.48 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.48 GOL.22: 4 residues within 4Å: Chain A: N.375, A.385, K.389, E.540 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.375, A:N.375, A:K.389, A:K.389 GOL.23: 5 residues within 4Å: Chain A: P.386, M.387, H.497, N.498 Ligands: HEC.18 5 PLIP interactions: 5 interactions with chain A Water bridges: A:S.493, A:G.494, A:N.498, A:N.498, A:Q.533 GOL.24: 7 residues within 4Å: Chain A: V.283, G.285, V.293, G.336, R.418 Ligands: HEC.12, HEC.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.283, A:G.285 GOL.25: 3 residues within 4Å: Chain A: P.325, T.364 Ligands: HEC.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.364, A:T.364

Links

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Citation

Santos-Silva, T. et al., Crystal Structure of the sixteen heme cytochrome from Desulfovibrio gigas. to be published

Release Date

2006-04-04

Peptides

sixteen heme cytochrome: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

sixteen heme cytochrome