SMTL ID : 8acq.1

S-layer Deinoxanthin-Binding Complex (SDBC), subunit DR_2577 assembled with its SOD DR_0644

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

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: 24 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 Chain E: L.53 11 PLIP interactions: 9 interactions with chain A, 1 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: A:V.527, A:P.540, A:I.542, A:A.569, A:I.571, A:A.579, A:A.609, A:L.611, E:L.53, C:L.1071 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: 24 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 Chain D: L.53 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: 8 interactions with chain C, 7 interactions with chain A Hydrophobic interactions: C:I.1076, C:V.1118, C:Y.1122, C:F.1127, C:Y.1129, A:F.523, A:V.525 Hydrogen bonds: C:R.268, C:Q.1157, A:Y.546, A:R.565, A:R.565, A:G.587 Salt bridges: C:R.268, A:R.565 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: 7 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:F.523, B:F.523, A:V.1118, A:F.1127, A:F.1127, A:Y.1129, A:F.1159 Hydrogen bonds: B:Y.546, B:Y.563, B:R.565, B:G.587, A:R.268, A:Q.1157 Salt bridges: B:R.565, A:R.268 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

12 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: 4 interactions with chain C, 1 interactions with chain B Metal complexes: C:R.549, C:G.551, C:D.553, C:G.559, B:E.381 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 CU.22: 4 residues within 4Å: Chain D: H.74, H.76, N.180, H.182 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.76, D:H.182, D:H.182 CU.23: 4 residues within 4Å: Chain E: H.74, H.76, N.180, H.182 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.74, E:H.76, E:H.182 CU.24: 4 residues within 4Å: Chain F: H.74, H.76, N.180, H.182 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.74, F:H.76, F:H.182

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 SDBC is active in quenching oxidative conditions and bridges the cell envelope layers in Deinococcus radiodurans. J.Biol.Chem. (2023)

Release Date

2023-04-12

Peptides

S-layer protein SlpA: ABC
DR_0644, only-Cu Superoxide Dismutase: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

E
I

F
L

Membrane

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

DR_0644, only-Cu Superoxide Dismutase

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