SMTL ID : 8c3f.1

Double mutant I(L177)H/F(M197)H structure of Photosynthetic Reaction Center From Cereibacter sphaeroides strain RV

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

EDO.1: 7 residues within 4Å: Chain A: C.108, G.112, I.113, G.114, Y.115 Chain B: R.228 Chain C: L.233 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:C.108, B:R.228, B:R.228 Water bridges: A:G.112 EDO.2: 2 residues within 4Å: Chain A: R.7 Chain C: E.37 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.7 Water bridges: A:S.4, A:R.7, A:R.7 EDO.14: 8 residues within 4Å: Chain A: H.116 Chain B: Y.3, Q.4, L.224, A.225, S.227, R.228 Chain C: Q.186 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.3, B:Q.4, B:S.227, B:S.227, B:R.228, B:R.228 EDO.18: 5 residues within 4Å: Chain B: Y.3, Q.4, N.5, I.6, F.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.4, B:N.5, B:I.6, B:F.7 EDO.32: 9 residues within 4Å: Chain B: S.227, R.228, F.229, G.230, R.233 Chain C: R.169, F.170, Q.186, C.226 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:R.169, C:Q.186, B:R.228, B:G.230, B:R.233 EDO.33: 3 residues within 4Å: Chain C: H.120, N.121, K.124 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:H.120, C:N.121, C:N.121, C:K.124 EDO.34: 3 residues within 4Å: Chain C: D.74, V.107, A.108 No protein-ligand interaction detected (PLIP)

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

DIO.3: 4 residues within 4Å: Chain A: F.123, L.235, S.239, F.242 No protein-ligand interaction detected (PLIP)

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

HTO.4: 2 residues within 4Å: Chain A: W.262, W.265 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.262, A:W.265, A:W.265, A:W.265 HTO.15: 7 residues within 4Å: Chain A: W.263, W.266 Chain B: R.87, L.89, F.90, F.91 Ligands: U10.7 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:W.266, B:F.90 Hydrogen bonds: B:L.89, B:F.90

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.5: 32 residues within 4Å: Chain A: F.97, F.121, 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, H.177, F.180, F.181, S.244, A.245, C.247, M.248 Chain B: Y.210 Ligands: BPB.6, BCL.13, BCL.16, LDA.17, BCL.19, U10.22 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:F.97, A:F.97, A:F.121, A:A.124, A:A.127, A:T.160, A:Y.162, A:F.167, A:F.167, A:A.176, A:H.177, A:F.180, A:F.180, A:F.181, B:Y.210 Hydrogen bonds: A:S.244 Metal complexes: A:H.173 BCL.13: 18 residues within 4Å: Chain A: H.168, M.174, H.177, T.178, F.181, T.182 Chain B: M.122, W.157, L.160, I.179, H.182, L.183, T.186 Ligands: BCL.5, U10.7, BCL.19, BPB.20, SPN.23 8 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: B:L.160, B:I.179, B:L.183, A:F.181, A:T.182 Metal complexes: B:H.182, H2O.1 pi-Stacking: A:H.177 BCL.16: 22 residues within 4Å: Chain A: I.46, Y.128, L.131, F.146, I.150, W.151, H.153, L.154, V.157 Chain B: H.197, G.203, I.206, A.207, Y.210, G.211, L.214 Ligands: BCL.5, BPB.6, LDA.17, BCL.19, U10.22, LDA.28 13 PLIP interactions: 6 interactions with chain B, 7 interactions with chain A, Hydrophobic interactions: B:I.206, B:I.206, B:A.207, B:Y.210, B:L.214, A:I.46, A:Y.128, A:L.131, A:F.146, A:L.154, A:V.157 pi-Stacking: B:Y.210 Metal complexes: A:H.153 BCL.19: 30 residues within 4Å: Chain A: V.157, Y.162, F.181 Chain B: V.126, A.153, I.154, L.156, W.157, L.160, T.186, N.187, F.189, S.190, N.195, L.196, H.197, H.202, S.205, I.206, L.209, Y.210, V.276, T.277, G.280, I.284 Ligands: BCL.5, BCL.13, BCL.16, BPB.20, LDA.31 18 PLIP interactions: 1 interactions with chain A, 17 interactions with chain B, Hydrophobic interactions: A:F.181, B:V.126, B:V.126, B:A.153, B:I.154, B:L.156, B:W.157, B:T.186, B:F.189, B:L.196, B:I.206, B:I.206, B:L.209, B:Y.210, B:V.276, B:T.277, B:I.284 Salt bridges: B:H.202

2 x BPB: BACTERIOPHEOPHYTIN B(Non-covalent)

BPB.6: 31 residues within 4Å: Chain A: T.38, F.41, A.42, I.49, A.93, A.96, F.97, W.100, E.104, I.117, A.120, F.121, F.123, A.124, Y.128, F.146, Y.148, G.149, I.150, H.153, L.238, V.241 Chain B: Y.210, A.213, L.214, M.218, W.252, M.256 Ligands: BCL.5, BCL.16, U10.22 20 PLIP interactions: 17 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:A.42, A:I.49, A:A.93, A:A.96, A:A.120, A:F.121, A:F.121, A:F.121, A:F.123, A:A.124, A:Y.128, A:F.146, A:Y.148, A:L.238, A:V.241, A:V.241, B:Y.210, B:A.213, B:L.214 Hydrogen bonds: A:E.104 BPB.20: 24 residues within 4Å: Chain A: F.181, A.184, L.185, L.189, L.219, V.220 Chain B: S.59, L.60, G.63, W.66, F.67, A.125, V.126, W.129, T.133, T.146, A.149, F.150, A.153, A.273, V.276, T.277 Ligands: BCL.13, BCL.19 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:W.66, B:F.67, B:W.129, B:W.129, B:A.149, B:F.150, B:F.150, B:F.150, B:V.276, B:T.277, A:A.184, A:L.189

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

U10.7: 23 residues within 4Å: Chain A: P.171, I.175, T.178, F.179, T.182, L.189, H.190, L.193, V.194, E.212, D.213, F.216, Y.222, S.223, I.224, G.225, T.226, I.229, L.232, L.236, W.263 Ligands: BCL.13, HTO.15 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:P.171, A:I.175, A:T.178, A:F.179, A:F.179, A:T.182, A:L.189, A:L.193, A:Y.222, A:I.224, A:I.224, A:I.229, A:I.229, A:L.232, A:L.232, A:L.236, A:W.263 Hydrogen bonds: A:I.224, A:G.225 U10.22: 27 residues within 4Å: Chain A: F.29, G.35, T.38, W.100, R.103 Chain B: L.214, 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, M.272 Ligands: BCL.5, BPB.6, BCL.16, LDA.17, LDA.36 14 PLIP interactions: 4 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:F.29, A:T.38, A:W.100, A:W.100, B:L.214, B:M.218, B:W.252, B:M.256, B:F.258, B:F.258, B:A.260, B:W.268, B:W.268 Hydrogen bonds: B:A.260

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

PO4.8: 2 residues within 4Å: Chain A: Y.73, K.82 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.73 Salt bridges: A:K.82 PO4.9: 5 residues within 4Å: Chain A: F.24, W.25 Chain C: E.86, G.87, F.88 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.25 Water bridges: A:G.27 PO4.26: 3 residues within 4Å: Chain B: N.28, G.53, S.54 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.28, B:S.54, B:S.54

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 1 residues within 4Å: Chain A: Y.67 No protein-ligand interaction detected (PLIP)

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

LDA.11: 6 residues within 4Å: Chain A: L.16, A.101, V.105, R.109, Y.115, P.118 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.101, A:V.105, A:Y.115, A:Y.115, A:P.118 LDA.12: 7 residues within 4Å: Chain A: V.220, G.221, Y.222 Chain B: G.31, V.32, G.33 Ligands: LDA.31 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.222 LDA.17: 7 residues within 4Å: Chain A: F.29 Chain B: M.256, G.257 Ligands: BCL.5, BCL.16, U10.22, LDA.36 No protein-ligand interaction detected (PLIP) LDA.28: 7 residues within 4Å: Chain B: P.200, L.204, F.208, M.272 Chain C: W.13 Ligands: BCL.16, LDA.36 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:F.208, C:W.13 Water bridges: B:G.203 LDA.29: 5 residues within 4Å: Chain B: F.7, T.8, L.38, W.41, F.42 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.41, B:F.42, B:F.42 pi-Cation interactions: B:W.41 LDA.30: 6 residues within 4Å: Chain B: L.167, L.285, L.286, G.288, T.289, V.290 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.167, B:L.285, B:L.286, B:T.289, B:V.290 LDA.31: 5 residues within 4Å: Chain A: V.220 Chain B: I.50, W.129 Ligands: LDA.12, BCL.19 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.50, B:W.129 LDA.36: 10 residues within 4Å: Chain B: R.253, F.258 Chain C: Q.24, Y.32, Q.45, G.46, F.48 Ligands: LDA.17, U10.22, LDA.28 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:F.48, C:F.48, B:F.258, B:F.258, B:F.258 Hydrogen bonds: B:R.253, B:R.253

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

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

1 x SPN: SPEROIDENONE(Non-covalent)

SPN.23: 24 residues within 4Å: Chain B: F.67, F.68, I.70, G.71, F.74, W.75, F.85, W.115, L.116, S.119, F.120, M.122, F.123, W.157, L.160, G.161, F.162, W.171, V.175, Y.177, G.178, I.179, H.182 Ligands: BCL.13 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.67, B:F.67, B:F.67, B:I.70, B:F.74, B:W.115, B:F.120, B:W.157, B:L.160, B:F.162, B:W.171, B:V.175, B:Y.177, B:I.179

2 x K: POTASSIUM ION(Non-covalent)

K.24: 2 residues within 4Å: Chain B: V.192, D.292 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:V.192, B:D.292 K.37: 3 residues within 4Å: Chain C: M.126, A.129, F.132 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:M.126, C:A.129, C:F.132, H2O.5

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.25: 4 residues within 4Å: Chain B: R.267, W.271 Chain C: Y.22 Ligands: CDL.27 Ligand excluded by PLIP

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.27: 19 residues within 4Å: Chain A: N.199, P.200 Chain B: G.143, K.144, H.145, W.148, W.155, R.267, I.270, W.271, L.278 Chain C: A.8, F.12, I.14, F.15, G.18, L.19, Y.22 Ligands: CL.25 22 PLIP interactions: 14 interactions with chain B, 7 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: B:W.148, B:W.148, B:W.155, B:W.155, B:W.155, B:I.270, B:W.271, B:L.278, C:I.14, C:F.15, C:F.15, C:F.15, C:L.19, C:Y.22, C:Y.22 Hydrogen bonds: B:K.144 Salt bridges: B:K.144, B:H.145, B:H.145, B:H.145, B:R.267, A:K.202

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

TRS.35: 3 residues within 4Å: Chain C: R.146, N.193, R.194 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.146, C:R.146, C:N.193, C:N.193, C:R.194, C:R.194

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fufina, T.Y. et al., Properties and Crystal Structure of the Cereibacter sphaeroides Photosynthetic Reaction Center with Double Amino Acid Substitution I(L177)H + F(M197)H. Membranes (Basel) (2023)

Release Date

2023-03-08

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
M

C
H

Membrane

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

Reaction center protein M chain

Reaction center protein H chain

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