SMTL ID : 6qvm.1

Undecaheme cytochrome from S-layer of Carboxydothermus ferrireducens

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

2 x NGA- NGA: 2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose(Post Translational Modification)

NGA-NGA.1: 5 residues within 4Å: Chain A: K.288, V.312, Y.333, N.338, Y.340 No protein-ligand interaction detected (PLIP) NGA-NGA.2: 2 residues within 4Å: Chain A: K.539, Y.541 No protein-ligand interaction detected (PLIP)

1 x NGA- NGA- NGA: 2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose

NGA-NGA-NGA.3: 3 residues within 4Å: Chain A: E.400, Y.411, L.573 No protein-ligand interaction detected (PLIP)

11 x HEC: HEME C(Covalent)

HEC.4: 19 residues within 4Å: Chain A: T.24, E.25, Y.27, A.28, T.31, K.33, N.34, C.35, C.38, H.39, M.60, L.69, T.70, I.75, L.77, F.84, M.85, K.89 Ligands: HEC.6 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:T.24, A:Y.27, A:A.28, A:T.31, A:K.33, A:I.75, A:L.77, A:F.84, A:M.85 Salt bridges: A:K.89 pi-Stacking: A:Y.27 Metal complexes: A:H.39 HEC.5: 16 residues within 4Å: Chain A: V.41, P.42, S.44, H.45, R.54, D.55, M.57, D.58, C.59, C.62, H.63, F.66, M.67, L.69, Q.74, I.75 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: A:P.42, A:R.54, A:M.57, A:F.66, A:L.69, A:I.75 Hydrogen bonds: A:S.44 Salt bridges: A:H.45 pi-Cation interactions: A:R.54 Metal complexes: A:H.45, A:H.63 HEC.6: 22 residues within 4Å: Chain A: T.72, V.82, M.85, A.224, K.228, C.229, C.232, H.233, C.351, E.352, H.355, G.358, H.361, A.362, G.365, P.367, I.370, L.371, G.372, K.374 Ligands: HEC.4, HEC.8 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:V.82, A:A.224, A:E.352, A:H.355, A:A.362, A:P.367, A:I.370, A:I.370, A:I.370 Hydrogen bonds: A:P.367 Water bridges: A:E.373, A:E.373, A:K.374 Salt bridges: A:H.233, A:K.374 Metal complexes: A:H.233, A:H.361 HEC.7: 20 residues within 4Å: Chain A: M.246, S.276, L.281, Y.289, H.306, Q.308, S.313, C.314, K.316, C.317, H.318, I.328, C.386, H.387, E.388, H.392, R.393, Y.584 Ligands: HEC.9, HEC.11 8 PLIP interactions: 7 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:L.281, A:Y.289, A:I.328, A:H.392 Hydrogen bonds: A:R.393 Water bridges: A:S.276 pi-Stacking: A:H.392 Metal complexes: H2O.4 HEC.8: 18 residues within 4Å: Chain A: C.229, Q.230, H.233, F.235, F.238, H.243, G.350, C.351, C.354, H.355, I.377, A.378, Q.437, V.474, P.479, H.480 Ligands: HEC.6, HEC.9 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:Q.230, A:H.233, A:F.235, A:F.235, A:F.235, A:F.235, A:F.235, A:F.238, A:F.238, A:I.377, A:V.474, A:P.479, A:P.479 Hydrogen bonds: A:Q.437 Water bridges: A:T.441 Salt bridges: A:H.480 Metal complexes: A:H.355, A:H.480 HEC.9: 22 residues within 4Å: Chain A: W.242, H.243, M.246, N.275, S.276, P.277, C.317, H.318, I.349, A.353, T.382, C.383, C.386, H.387, C.473, V.474, H.477, P.479, K.487 Ligands: HEC.7, HEC.8, HEC.11 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:W.242, A:I.349, A:I.349, A:A.353, A:V.474, A:H.477, A:P.479 Hydrogen bonds: A:W.242, A:K.487 Water bridges: A:K.487, A:K.487, A:Q.488 Salt bridges: A:K.487 Metal complexes: A:H.243, A:H.387 HEC.10: 14 residues within 4Å: Chain A: T.420, I.421, N.424, H.426, C.431, C.434, H.435, C.500, H.501, H.517, Q.519, A.652 Ligands: HEC.12, HEC.13 5 PLIP interactions: 5 interactions with chain A, Hydrophobic interactions: A:T.420 Hydrogen bonds: A:Q.519, A:A.652 pi-Stacking: A:H.517 Metal complexes: A:H.435 HEC.11: 23 residues within 4Å: Chain A: C.383, E.384, H.387, R.393, G.394, G.395, Y.397, I.471, T.472, C.473, C.476, H.477, K.487, L.489, L.496, V.550, M.554, G.557, H.559, F.561 Ligands: HEC.7, HEC.9, HEC.12 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:E.384, A:H.387, A:R.393, A:Y.397, A:I.471, A:K.487, A:L.489, A:L.496, A:V.550, A:F.561 Hydrogen bonds: A:G.557 Salt bridges: A:K.487 Metal complexes: A:H.477, A:H.559 HEC.12: 20 residues within 4Å: Chain A: K.413, H.414, I.416, S.417, T.420, C.434, H.435, I.471, T.475, L.496, C.497, C.500, H.501, H.553, M.554, F.561, K.562 Ligands: HEC.10, HEC.11, HEC.13 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:K.413, A:I.471, A:T.475, A:H.553, A:F.561, A:F.561 Hydrogen bonds: A:K.413, A:I.416, A:T.420 Salt bridges: A:K.562 pi-Stacking: A:F.561 Metal complexes: A:H.414, A:H.501 HEC.13: 20 residues within 4Å: Chain A: C.497, M.498, H.501, Q.519, F.523, M.544, A.547, E.548, C.549, C.552, H.553, V.563, K.565, A.654, S.655, I.658, H.659 Ligands: HEC.10, HEC.12, HEC.14 10 PLIP interactions: 10 interactions with chain A, Hydrophobic interactions: A:H.501, A:Q.519, A:F.523, A:F.523, A:A.547, A:V.563 Hydrogen bonds: A:V.563 Salt bridges: A:K.565 Metal complexes: A:H.553, A:H.659 HEC.14: 16 residues within 4Å: Chain A: M.544, S.546, A.547, T.551, C.552, V.563, G.564, S.594, C.595, C.598, H.599, F.604, V.609, W.612, I.658 Ligands: HEC.13 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:T.551, A:V.563, A:F.604, A:F.604, A:V.609, A:W.612, A:I.658 Metal complexes: A:H.599

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.15: 6 residues within 4Å: Chain A: T.368, K.369, I.370, L.371, K.374, D.375 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.368, A:K.374, A:K.374 Water bridges: A:P.357, A:L.371

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.16: 6 residues within 4Å: Chain A: I.328, E.384, K.385, D.578, S.580, L.581 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.384, A:S.580, A:S.580 GOL.17: 5 residues within 4Å: Chain A: Q.437, R.440, T.441, T.475, R.490 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.437, A:R.440, A:T.475

1 x CA: CALCIUM ION(Non-covalent)

CA.18: 4 residues within 4Å: Chain A: E.384, G.395, N.398, D.399 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.384, A:G.395, A:D.399, H2O.2, H2O.8

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.19: 6 residues within 4Å: Chain A: S.478, P.479, H.480, S.481, K.483, R.490 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.478, A:S.478 Salt bridges: A:H.480, A:K.483, A:R.490

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tikhonova, T.V. et al., Extracellular Fe(III) reductase structure reveals a modular organization enabling S-layer insertion and electron transfer to insoluble substrates. Structure (2023)

Release Date

2020-03-25

Peptides

Multiheme cytochrome cf: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Multiheme cytochrome cf