SMTL ID : 8c87.1

Double mutant A(L172)C/L(L246)C structure of Photosynthetic Reaction Center From Cereibacter sphaeroides strain RV

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

hetero-1-1-1-mer

Ligands

12 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)

LDA.1: 10 residues within 4Å: Chain A: Q.23, Y.31, Q.44, F.47 Chain C: R.253, G.257, F.258, W.268 Ligands: U10.23, LDA.31 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:F.258, C:F.258, C:F.258, C:F.258, C:W.268, A:F.47, A:F.47 Hydrogen bonds: C:R.253, C:R.253 LDA.5: 6 residues within 4Å: Chain A: A.16, I.19, Y.20 Ligands: UNL.2, LDA.6, CDL.19 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.19, A:Y.20, A:Y.20, A:Y.20 LDA.6: 5 residues within 4Å: Chain A: Y.20, P.46, F.47, P.48 Ligands: LDA.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.46, A:F.47 LDA.7: 8 residues within 4Å: Chain A: N.197, L.232, R.239 Chain B: V.105, R.109, Y.115, F.119 Chain C: E.2 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B, 1 interactions with chain A Salt bridges: C:E.2 Hydrophobic interactions: B:V.105, B:Y.115 Hydrogen bonds: A:N.197 LDA.13: 7 residues within 4Å: Chain B: V.220, G.221 Chain C: S.30, G.31, V.32, G.48, I.50 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.50 LDA.18: 8 residues within 4Å: Chain B: L.75, G.76, Q.87, T.90, I.91, T.94, L.133, W.142 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Q.87, B:T.90, B:I.91, B:L.133, B:L.133, B:W.142, B:W.142 LDA.25: 13 residues within 4Å: Chain A: W.12, L.15, L.18, I.19 Chain C: P.200, G.203, L.204, A.207, F.208, W.268, M.272 Ligands: UNL.2, BCL.11 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:W.12, A:W.12, A:L.15, A:L.18, A:I.19, C:F.208, C:W.268 LDA.26: 4 residues within 4Å: Chain C: F.7, T.8, W.41, F.42 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.7, C:F.7, C:W.41, C:F.42, C:F.42 pi-Cation interactions: C:W.41 LDA.27: 6 residues within 4Å: Chain C: F.105, A.107, G.113, L.116, I.117, F.120 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.120 LDA.28: 4 residues within 4Å: Chain C: R.13, P.34, F.35, T.37 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:P.34 Hydrogen bonds: C:T.37 LDA.31: 9 residues within 4Å: Chain B: P.28, F.29 Chain C: M.256, G.257, F.258 Ligands: LDA.1, BCL.10, BCL.11, U10.23 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.258, C:F.258 LDA.32: 2 residues within 4Å: Chain C: L.52, W.129 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.52, C:W.129

5 x UNL: UNKNOWN LIGAND

UNL.2: 7 residues within 4Å: Chain A: W.12, I.13, L.15, I.19 Ligands: UNL.3, LDA.5, LDA.25 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.13, A:L.15, A:I.19 UNL.3: 5 residues within 4Å: Chain A: Y.9, W.12 Ligands: UNL.2, BCL.11, HTO.17 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.9, A:W.12 UNL.14: 5 residues within 4Å: Chain B: T.130, F.134, M.138, F.242, C.246 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.134, B:F.242 UNL.15: 6 residues within 4Å: Chain B: Y.115, H.116, F.119 Chain C: E.2, Q.4, I.6 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:E.2, C:Q.4, C:I.6, B:Y.115, B:Y.115, B:Y.115, B:F.119, B:F.119 UNL.29: 3 residues within 4Å: Chain C: L.167, T.289, V.290 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.167, C:V.290

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 3 residues within 4Å: Chain A: Q.190, S.191, N.192 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.191, A:N.192 EDO.30: 8 residues within 4Å: Chain A: Q.185 Chain B: H.116 Chain C: Y.3, Q.4, L.224, A.225, S.227, R.228 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.3, C:S.227, C:R.228, C:R.228

1 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.8: 13 residues within 4Å: Chain B: T.182, L.189, H.190, L.193, E.212, D.213, F.216, S.223, I.224, G.225, T.226, I.229, L.232 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:T.182, B:F.216, B:F.216, B:I.229, B:L.232 Hydrogen bonds: B:S.223, B:I.224, B:G.225 Salt bridges: B:H.190

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.9: 20 residues within 4Å: Chain B: H.168, M.174, I.177, T.178, F.181, T.182, L.185 Chain C: W.66, F.67, M.122, W.157, V.175, I.179, H.182, L.183, T.186 Ligands: BCL.10, BCL.20, BPH.21, SPN.24 12 PLIP interactions: 6 interactions with chain C, 6 interactions with chain B, Hydrophobic interactions: C:W.66, C:F.67, C:F.67, C:V.175, C:L.183, B:I.177, B:I.177, B:F.181, B:F.181, B:L.185 Metal complexes: C:H.182 pi-Stacking: B:F.181 BCL.10: 31 residues within 4Å: Chain B: F.97, A.124, I.125, A.127, Y.128, L.131, W.156, V.157, S.158, T.160, G.161, Y.162, N.166, F.167, H.168, H.173, A.176, I.177, F.180, S.244, A.245, C.247, M.248 Chain C: F.197, Y.210 Ligands: BCL.9, BCL.11, BPH.12, BCL.20, U10.23, LDA.31 17 PLIP interactions: 14 interactions with chain B, 3 interactions with chain C, Hydrophobic interactions: B:F.97, B:A.124, B:A.127, B:V.157, B:T.160, B:Y.162, B:F.167, B:F.167, B:A.176, B:I.177, B:F.180, B:F.180, C:F.197, C:F.197, C:Y.210 Hydrogen bonds: B:S.244 Metal complexes: B:H.173 BCL.11: 25 residues within 4Å: Chain B: I.46, I.49, Y.128, L.131, F.146, I.150, W.151, H.153, L.154, V.157 Chain C: F.197, G.203, I.206, A.207, Y.210, G.211, L.214 Ligands: UNL.3, BCL.10, BPH.12, HTO.17, BCL.20, U10.23, LDA.25, LDA.31 13 PLIP interactions: 7 interactions with chain B, 6 interactions with chain C, Hydrophobic interactions: B:I.46, B:I.49, B:Y.128, B:L.131, B:F.146, B:L.154, C:F.197, C:I.206, C:I.206, C:Y.210, C:L.214 Metal complexes: B:H.153 pi-Stacking: C:Y.210 BCL.20: 27 residues within 4Å: Chain B: V.157, Y.162, H.168, F.181 Chain C: M.122, A.153, I.154, L.156, W.157, L.160, T.186, N.187, F.189, S.190, L.196, F.197, H.202, S.205, I.206, Y.210, V.276, G.280, I.284 Ligands: BCL.9, BCL.10, BCL.11, BPH.21 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain B, Hydrophobic interactions: C:A.153, C:L.156, C:W.157, C:T.186, C:F.189, C:L.196, C:I.206, C:Y.210, C:V.276, B:F.181 Metal complexes: C:H.202

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.12: 29 residues within 4Å: Chain B: T.38, A.42, I.49, A.93, A.96, F.97, W.100, E.104, I.117, A.120, F.121, A.124, Y.128, Y.148, G.149, I.150, L.238, V.241 Chain C: Y.210, A.213, L.214, A.217, M.218, W.252, M.256 Ligands: BCL.10, BCL.11, HTO.17, U10.23 15 PLIP interactions: 3 interactions with chain C, 12 interactions with chain B Hydrophobic interactions: C:Y.210, C:A.213, C:A.217, B:A.42, B:I.49, B:A.96, B:A.120, B:F.121, B:F.121, B:F.121, B:Y.128, B:Y.148, B:L.238, B:V.241, B:V.241 BPH.21: 26 residues within 4Å: Chain B: F.181, A.184, L.185, A.188, L.189, L.219, V.220 Chain C: S.59, L.60, G.63, L.64, W.66, F.67, A.125, V.126, W.129, T.133, T.146, A.149, F.150, A.153, A.273, V.274, T.277 Ligands: BCL.9, BCL.20 15 PLIP interactions: 13 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:L.60, C:W.66, C:F.67, C:F.67, C:A.125, C:W.129, C:W.129, C:A.149, C:F.150, C:F.150, C:F.150, C:A.153, C:A.273, B:A.184, B:L.189

2 x HTO: HEPTANE-1,2,3-TRIOL(Non-covalent)

HTO.16: 5 residues within 4Å: Chain B: M.138, M.139, G.140, T.253, F.256 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.256 Hydrogen bonds: B:M.138 HTO.17: 7 residues within 4Å: Chain B: P.61, I.64, Y.148, I.150 Ligands: UNL.3, BCL.11, BPH.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.61, B:Y.148

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.19: 17 residues within 4Å: Chain A: I.13, F.14, G.17, L.18, Y.21 Chain B: N.199 Chain C: G.143, K.144, H.145, W.148, L.151, W.155, R.267, W.271, V.274, L.278 Ligands: LDA.5 23 PLIP interactions: 17 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: C:W.148, C:W.148, C:W.148, C:W.148, C:W.155, C:W.155, C:W.155, C:W.271, C:W.271, C:V.274, C:L.278, A:I.13, A:F.14, A:F.14, A:F.14, A:Y.21, A:Y.21 Hydrogen bonds: C:K.144 Salt bridges: C:K.144, C:H.145, C:H.145, C:H.145, C:R.267

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

FE.22: 5 residues within 4Å: Chain B: H.190, H.230 Chain C: H.219, E.234, H.266 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Metal complexes: B:H.190, B:H.230, C:H.219, C:E.234, C:H.266

1 x U10: UBIQUINONE-10(Non-covalent)

U10.23: 25 residues within 4Å: Chain B: F.29, Y.30, G.35, W.100, R.103 Chain C: L.214, M.218, H.219, T.222, A.248, A.249, W.252, M.256, F.258, N.259, A.260, T.261, I.265, W.268, M.272 Ligands: LDA.1, BCL.10, BCL.11, BPH.12, LDA.31 17 PLIP interactions: 14 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:L.214, C:M.218, C:H.219, C:W.252, C:M.256, C:F.258, C:F.258, C:I.265, C:I.265, C:W.268, C:W.268, C:W.268, B:F.29, B:F.29, B:F.29 Hydrogen bonds: C:T.222, C:A.260

1 x SPN: SPEROIDENONE(Non-covalent)

SPN.24: 21 residues within 4Å: Chain C: F.67, F.68, G.71, F.74, W.75, L.89, F.105, L.116, S.119, F.120, M.122, F.123, W.157, G.161, F.162, W.171, V.175, Y.177, G.178, I.179 Ligands: BCL.9 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:F.67, C:F.67, C:F.67, C:F.68, C:F.74, C:L.89, C:F.105, C:F.120, C:W.157, C:F.162, C:F.162, C:F.162, C:W.171, C:V.175, C:V.175, C:Y.177, C:Y.177, C:I.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Selikhanov, G. et al., Stabilization of Cereibacter sphaeroides Photosynthetic Reaction Center by the Introduction of Disulfide Bonds. Membranes (Basel) (2023)

Release Date

2023-11-22

Peptides

Reaction center protein H chain: A
Reaction center protein L chain: B
Reaction center protein M chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
M

Membrane

We predict this structure to be a membrane protein.
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Reaction center protein H chain

Reaction center protein L chain

Reaction center protein M chain

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