SMTL ID : 7zgy.1

S-layer Deinoxanthin Binding Complex, C3 symmetry

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

3 x JPI: (3~{S},5~{R},6~{R})-5-[(3~{S},7~{R},12~{S},16~{S},20~{S})-3,7,12,16,20,24-hexamethyl-24-oxidanyl-pentacosyl]-4,4,6-trimethyl-cyclohexane-1,3-diol(Non-covalent)

JPI.1: 23 residues within 4Å: Chain A: P.494, V.527, D.528, G.529, V.532, P.540, Q.541, I.542, A.569, Q.570, I.571, A.579, G.580, I.581, A.609, D.610, L.611, S.622, E.623, Y.624, F.644 Chain C: L.1070, L.1071 10 PLIP interactions: 1 interactions with chain C, 9 interactions with chain A Hydrophobic interactions: C:L.1071, A:V.527, A:P.540, A:I.542, A:A.569, A:I.571, A:A.579, A:A.609, A:L.611 Hydrogen bonds: A:S.622 JPI.9: 23 residues within 4Å: Chain A: L.1070, L.1071 Chain B: P.494, V.527, D.528, G.529, V.532, P.540, Q.541, I.542, A.569, Q.570, I.571, A.579, G.580, I.581, A.609, D.610, L.611, S.622, E.623, Y.624, F.644 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:V.527, B:V.532, B:P.540, B:I.542, B:A.579, B:I.581, B:A.609, B:L.611, B:F.644 Hydrogen bonds: B:S.622 JPI.16: 23 residues within 4Å: Chain B: L.1070, L.1071 Chain C: P.494, V.527, D.528, G.529, V.532, P.540, Q.541, I.542, A.569, Q.570, I.571, A.579, G.580, I.581, A.609, D.610, L.611, S.622, E.623, Y.624, F.644 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:V.532, C:P.540, C:I.542, C:I.571, C:I.581, C:L.611, C:Y.624, B:L.1071 Hydrogen bonds: C:S.622, C:S.622

3 x JQ6: [(2~{S})-2-acetyloxy-3-[[(2~{S})-3-[(2~{R},3~{S},4~{S},5~{S},6~{S})-6-(hydroxymethyl)-3-(octadecanoylamino)-4,5-bis(oxidanyl)oxan-2-yl]oxy-1-oxidanylidene-1-(pentylamino)propan-2-yl]oxy-oxidanyl-phosphoryl]oxy-propyl] ethanoate(Non-covalent)(Covalent)

JQ6.2: 19 residues within 4Å: Chain A: V.525, I.542, K.543, G.544, V.545, R.565, G.566, V.567, Y.583, Q.585, G.587, R.588, S.602, D.603, T.605, Y.607, R.628, R.630 Ligands: JPX.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.583, A:Y.583, A:D.603 Hydrogen bonds: A:Y.583, A:Q.585, A:T.605, A:R.628, A:R.628 Salt bridges: A:R.565, A:R.565 JQ6.11: 18 residues within 4Å: Chain B: F.523, G.544, V.545, R.565, G.566, V.567, Y.583, Q.585, G.587, R.588, S.602, D.603, T.605, Y.607, R.628, R.630, V.638 Ligands: JPX.8 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:R.565, B:R.565, B:Y.583, B:D.603 Hydrogen bonds: B:Q.585, B:Q.585, B:T.605, B:T.605, B:R.628 Salt bridges: B:R.565, B:R.565 JQ6.17: 22 residues within 4Å: Chain C: F.523, V.525, I.542, G.544, V.545, Y.546, R.565, G.566, V.567, Y.583, Q.585, G.587, R.588, S.602, D.603, V.604, T.605, Y.607, R.628, R.630, V.638 Ligands: JPX.10 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:Y.583, C:Y.583, C:D.603 Hydrogen bonds: C:Q.585, C:D.603, C:T.605, C:Y.607, C:R.630 Salt bridges: C:R.565, C:R.565

3 x JPX: [(2~{S})-3-[[(2~{S})-3-[(2~{S},3~{S},4~{S},5~{S},6~{S})-6-(hydroxymethyl)-4,5-bis(oxidanyl)-3-(propanoylamino)oxan-2-yl]oxy-1-oxidanylidene-1-(pentadecylamino)propan-2-yl]oxy-oxidanyl-phosphoryl]oxy-2-octanoyloxy-propyl] decanoate(Non-covalent)

JPX.3: 24 residues within 4Å: Chain A: V.495, V.497, F.523, V.525, Y.546, Y.563, R.565, Q.585, E.586, G.587, R.588, D.589, D.603 Chain C: R.268, I.1076, V.1118, G.1120, A.1121, Y.1122, F.1127, Y.1129, Q.1157, F.1159 Ligands: JQ6.2 15 PLIP interactions: 7 interactions with chain A, 8 interactions with chain C Hydrophobic interactions: A:F.523, A:V.525, C:I.1076, C:V.1118, C:Y.1122, C:F.1127, C:Y.1129 Hydrogen bonds: A:Y.546, A:R.565, A:R.565, A:G.587, C:R.268, C:Q.1157 Salt bridges: A:R.565, C:R.268 JPX.8: 26 residues within 4Å: Chain A: R.268, T.1074, K.1075, I.1076, V.1118, E.1119, G.1120, A.1121, Y.1122, F.1127, Y.1129, Q.1157, F.1159 Chain B: V.497, F.523, V.525, Y.546, Y.563, Y.564, R.565, Q.585, E.586, G.587, R.588, D.589 Ligands: JQ6.11 15 PLIP interactions: 8 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:V.1118, A:F.1127, A:F.1127, A:Y.1129, A:F.1159, B:F.523, B:F.523 Hydrogen bonds: A:R.268, A:Q.1157, B:Y.546, B:Y.563, B:R.565, B:G.587 Salt bridges: A:R.268, B:R.565 JPX.10: 27 residues within 4Å: Chain B: R.268, L.1071, T.1074, K.1075, I.1076, V.1118, G.1120, A.1121, Y.1122, F.1127, Y.1129, Q.1157, F.1159 Chain C: V.495, V.497, F.523, V.525, Y.546, Y.563, Y.564, R.565, Q.585, E.586, G.587, R.588, D.589 Ligands: JQ6.17 15 PLIP interactions: 7 interactions with chain C, 8 interactions with chain B Hydrophobic interactions: C:F.523, C:F.523, C:Y.546, B:V.1118, B:F.1127, B:F.1127, B:Y.1129, B:Y.1129 Hydrogen bonds: C:Y.546, C:Y.563, C:R.565, B:Q.1157, B:Q.1157 Salt bridges: C:R.565, B:R.268

9 x CU: COPPER (II) ION(Non-covalent)

CU.4: 7 residues within 4Å: Chain A: S.548, R.549, G.551, D.553, G.559, Y.560 Chain C: E.381 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Metal complexes: A:R.549, A:G.551, A:G.559, C:E.381 CU.5: 3 residues within 4Å: Chain A: D.513, N.515, G.716 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.513, A:D.513, A:G.716 CU.6: 5 residues within 4Å: Chain A: D.274, D.276, R.305, F.308, D.310 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.274, A:D.276, A:R.305, A:F.308, A:D.310 CU.12: 7 residues within 4Å: Chain A: E.381 Chain B: S.548, R.549, G.551, D.553, G.559, Y.560 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Metal complexes: B:R.549, B:G.551, B:G.559, A:E.381 CU.13: 3 residues within 4Å: Chain B: D.513, N.515, G.716 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.513, B:D.513, B:G.716 CU.14: 5 residues within 4Å: Chain B: D.274, D.276, R.305, F.308, D.310 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.274, B:D.276, B:R.305, B:F.308, B:D.310 CU.18: 7 residues within 4Å: Chain B: E.381 Chain C: S.548, R.549, G.551, D.553, G.559, Y.560 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain C Metal complexes: B:E.381, C:R.549, C:G.551, C:D.553, C:G.559 CU.19: 3 residues within 4Å: Chain C: D.513, N.515, G.716 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.513, C:D.513, C:G.716 CU.20: 5 residues within 4Å: Chain C: D.274, D.276, R.305, F.308, D.310 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.274, C:D.276, C:R.305, C:F.308, C:D.310

3 x FE: FE (III) ION(Non-covalent)

FE.7: 6 residues within 4Å: Chain A: D.438, N.440, N.442, K.444, D.446, E.449 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.438, A:K.444, A:D.446 FE.15: 6 residues within 4Å: Chain B: D.438, N.440, N.442, K.444, D.446, E.449 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.438, B:K.444, B:D.446 FE.21: 6 residues within 4Å: Chain C: D.438, N.440, N.442, K.444, D.446, E.449 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.438, C:K.444, C:D.446

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Farci, D. et al., The cryo-EM structure of the S-layer deinoxanthin-binding complex of Deinococcus radiodurans informs properties of its environmental interactions. J.Biol.Chem. (2022)

Release Date

2022-07-13

Peptides

S-layer protein SlpA: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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S-layer protein SlpA

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