SMTL ID : 8c88.1

Double mutant G(M19)C/T(L214)C structure of Photosynthetic Reaction Center From Cereibacter sphaeroides strain RV

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x NKP: (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate(Non-covalent)

NKP.1: 11 residues within 4Å: Chain A: I.14, F.15, A.17, G.18, L.19, Y.22 Chain B: N.199 Chain C: H.145, R.267 Ligands: UNL.3, NKP.17 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:F.15, A:A.17, A:L.19, A:Y.22, A:Y.22 Salt bridges: C:H.145, C:R.267 NKP.17: 12 residues within 4Å: Chain C: G.143, K.144, H.145, W.148, L.151, S.152, W.155, I.270, W.271, V.274, L.278 Ligands: NKP.1 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:W.148, C:W.155, C:W.155, C:W.155, C:W.155, C:I.270, C:W.271, C:V.274, C:L.278 Hydrogen bonds: C:K.144 Salt bridges: C:H.145

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

LDA.2: 9 residues within 4Å: Chain A: Q.24, Y.32, Q.45, F.48 Chain C: R.253, F.258 Ligands: U10.22, LDA.24, LDA.31 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:F.258, C:F.258, A:F.48, A:F.48 Hydrogen bonds: C:R.253, C:R.253 LDA.24: 11 residues within 4Å: Chain A: W.13, I.20 Chain C: P.200, G.203, L.204, A.207, W.268, M.272 Ligands: LDA.2, UNL.5, BCL.8 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:A.207, C:W.268, A:W.13, A:W.13, A:I.20 LDA.25: 4 residues within 4Å: Chain C: F.7, T.8, L.38, W.41 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.7, C:F.7, C:W.41, C:W.41 pi-Cation interactions: C:W.41 LDA.26: 7 residues within 4Å: Chain C: F.105, A.106, A.107, L.109, L.116, I.117, F.120 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.120, C:F.120 LDA.27: 8 residues within 4Å: Chain C: R.13, V.32, G.33, P.34, F.35, S.36, T.37, L.38 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.36, C:T.37, C:L.38 LDA.31: 7 residues within 4Å: Chain C: M.256, G.257, F.258 Ligands: LDA.2, UNL.5, BCL.8, U10.22 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.258

7 x UNL: UNKNOWN LIGAND

UNL.3: 5 residues within 4Å: Chain A: Y.21, P.47, F.48, P.49 Ligands: NKP.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.21, A:P.47, A:F.48 UNL.4: 4 residues within 4Å: Chain A: Y.10, W.13, A.17, I.20 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.10, A:W.13, A:W.13, A:W.13, A:A.17, A:I.20 UNL.5: 4 residues within 4Å: Chain A: W.13 Ligands: BCL.8, LDA.24, LDA.31 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.13 UNL.10: 5 residues within 4Å: Chain B: Q.87, T.90, I.91, L.133, W.142 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:T.90, B:I.91, B:L.133, B:W.142, B:W.142, B:W.142 UNL.11: 5 residues within 4Å: Chain B: L.16, A.101, V.105, Y.115 Ligands: UNL.28 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.16, B:A.101, B:V.105, B:Y.115, B:Y.115, B:Y.115 UNL.12: 5 residues within 4Å: Chain B: F.134, M.138, F.242, I.249 Ligands: EDO.15 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.134, B:F.242, B:I.249 UNL.28: 5 residues within 4Å: Chain B: Y.115, F.119 Chain C: E.2, Q.4 Ligands: UNL.11 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:F.119, B:F.119, C:E.2

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

OLC.6: 17 residues within 4Å: Chain B: L.189, H.190, L.193, E.212, D.213, F.216, V.220, G.221, Y.222, S.223, I.224, G.225, T.226, I.229, L.232 Chain C: L.47, G.48 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:L.189, B:F.216, B:F.216, B:Y.222, B:Y.222, B:I.229, B:L.232, C:L.47 Hydrogen bonds: B:E.212, B:E.212, B:S.223, B:I.224, B:G.225

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.7: 29 residues within 4Å: Chain B: F.97, F.121, A.124, I.125, A.127, Y.128, L.131, W.156, V.157, S.158, T.160, G.161, N.166, F.167, H.168, H.173, A.176, I.177, F.180, S.244, A.245, C.247, M.248 Chain C: Y.210 Ligands: BCL.8, BPH.9, BCL.18, BCL.19, U10.22 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:F.97, B:F.97, B:F.121, B:A.124, B:A.127, B:T.160, B:F.167, B:F.167, B:A.176, B:I.177, B:F.180, B:F.180, C:Y.210 Hydrogen bonds: B:S.244 Metal complexes: B:H.173 BCL.8: 20 residues within 4Å: Chain B: I.46, Y.128, F.146, I.150, H.153, L.154 Chain C: F.197, G.203, I.206, A.207, Y.210, G.211, L.214 Ligands: UNL.5, BCL.7, BPH.9, BCL.19, U10.22, LDA.24, LDA.31 11 PLIP interactions: 6 interactions with chain C, 5 interactions with chain B, Hydrophobic interactions: C:F.197, C:I.206, C:I.206, C:Y.210, C:L.214, B:I.46, B:Y.128, B:F.146, B:L.154 pi-Stacking: C:Y.210 Metal complexes: B:H.153 BCL.18: 20 residues within 4Å: Chain B: H.168, M.174, I.177, T.178, F.181, T.182 Chain C: W.66, F.67, L.89, M.122, W.157, L.160, I.179, H.182, L.183, T.186 Ligands: BCL.7, BCL.19, BPH.20, SPN.23 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain B, Hydrophobic interactions: C:W.66, C:F.67, C:L.89, C:L.160, C:L.183, B:I.177, B:I.177 Metal complexes: C:H.182 BCL.19: 26 residues within 4Å: Chain B: V.157, Y.162, H.168, F.181 Chain C: V.126, A.153, 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.7, BCL.8, BCL.18, BPH.20 10 PLIP interactions: 10 interactions with chain C, Hydrophobic interactions: C:V.126, C:A.153, C:L.156, C:W.157, C:T.186, C:N.187, C:F.189, C:I.206, C:V.276 Metal complexes: C:H.202

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.9: 30 residues within 4Å: Chain B: F.41, A.42, I.49, C.92, A.93, A.96, F.97, W.100, E.104, I.117, A.120, F.121, F.123, A.124, Y.128, Y.148, G.149, I.150, H.153, L.238, V.241 Chain C: Y.210, A.213, L.214, M.218, W.252, M.256 Ligands: BCL.7, BCL.8, U10.22 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:I.49, B:A.120, B:F.121, B:F.121, B:F.121, B:F.123, B:Y.148, B:Y.148, B:L.238, B:V.241, C:A.213, C:L.214 Hydrogen bonds: B:E.104 BPH.20: 22 residues within 4Å: Chain B: F.181, A.184, L.185, L.189, L.219, V.220 Chain C: S.59, G.63, L.64, W.66, F.67, A.125, V.126, W.129, T.146, A.149, F.150, A.153, A.273, T.277 Ligands: BCL.18, BCL.19 17 PLIP interactions: 14 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:L.64, C:W.66, C:F.67, C:F.67, C:F.67, C:F.67, C:W.129, C:W.129, C:A.149, C:F.150, C:F.150, C:F.150, C:A.153, C:T.277, B:A.184, B:L.185, B:L.189

1 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)

DIO.13: 3 residues within 4Å: Chain B: W.266 Chain C: L.86, F.90 1 PLIP interactions: 1 interactions with chain C Water bridges: C:F.90

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

EDO.14: 2 residues within 4Å: Chain B: S.239, F.242 No protein-ligand interaction detected (PLIP) EDO.15: 3 residues within 4Å: Chain B: L.126, A.245 Ligands: UNL.12 No protein-ligand interaction detected (PLIP) EDO.16: 7 residues within 4Å: Chain A: L.233 Chain B: G.112, I.113, G.114, Y.115 Chain C: E.2, R.228 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.228, C:R.228

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

FE.21: 5 residues within 4Å: Chain B: H.190, H.230 Chain C: H.219, E.234, H.266 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Metal complexes: C:H.219, C:E.234, C:H.266, B:H.190, B:H.230

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

U10.22: 26 residues within 4Å: Chain B: F.29, G.35, T.38, F.39, W.100, R.103 Chain C: M.218, H.219, T.222, I.223, A.248, A.249, W.252, M.256, F.258, N.259, A.260, T.261, M.262, I.265, W.268 Ligands: LDA.2, BCL.7, BCL.8, BPH.9, LDA.31 17 PLIP interactions: 12 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:M.218, 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:T.38, B:F.39, B:W.100, B:W.100 Hydrogen bonds: C:T.222, C:A.260

1 x SPN: SPEROIDENONE(Non-covalent)

SPN.23: 24 residues within 4Å: Chain C: F.67, F.68, I.70, G.71, I.72, F.74, W.75, L.89, W.115, L.116, S.119, F.120, M.122, W.157, L.160, G.161, F.162, W.171, V.175, Y.177, G.178, I.179, H.182 Ligands: BCL.18 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:F.67, C:F.67, C:F.67, C:F.68, C:I.70, C:F.74, C:F.74, C:L.89, C:W.115, C:F.120, C:L.160, 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, C:H.182

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

PO4.29: 4 residues within 4Å: Chain C: N.28, Y.51, G.53, S.54 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.28, C:Y.51, C:S.54 PO4.30: 5 residues within 4Å: Chain C: Y.3, Q.4, N.5, I.6, F.7 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.4, C:I.6, C:F.7

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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