SMTL ID : 7q7m.1

Room temperature structure of the Rhodobacter Sphaeroides Photosynthetic Reaction Center F(M197)H mutant at 100 MPa helium gas pressure in a sapphire capillary

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

LDA.1: 17 residues within 4Å: Chain A: I.19, Q.23, M.27, Y.31, L.33, Q.44, G.45, P.46, F.47 Chain C: R.253, G.257, F.258, W.268 Ligands: BCL.5, UQ7.11, LDA.16, LDA.21 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:F.47, C:F.258, C:F.258, C:W.268 Hydrogen bonds: A:Y.31, C:R.253 LDA.2: 8 residues within 4Å: Chain A: S.10, I.13, F.14, G.17, L.18, Y.21 Chain C: W.271 Ligands: LDA.3 7 PLIP interactions: 1 interactions with chain C, 6 interactions with chain A Hydrogen bonds: C:W.271 Hydrophobic interactions: A:I.13, A:F.14, A:L.18 Water bridges: A:Y.21, A:Y.21 pi-Cation interactions: A:Y.21 LDA.3: 12 residues within 4Å: Chain A: L.3, L.6, A.7, S.10, F.11, F.14 Chain C: F.201, W.271, L.278, I.282 Ligands: LDA.2, LDA.17 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.6, A:A.7 LDA.8: 11 residues within 4Å: Chain B: L.16, V.98, A.101, L.102, V.105, R.109, Y.115, P.118, F.119, A.122, I.125 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.101, B:Y.115, B:A.122 Hydrogen bonds: B:R.109 LDA.9: 13 residues within 4Å: Chain B: F.41, G.77, W.86, Q.87, T.90, I.91, T.94, G.95, L.129, V.132, L.133, W.142 Ligands: LDA.10 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:T.90, B:I.91, B:W.142, B:W.142 LDA.10: 12 residues within 4Å: Chain B: F.22, F.33, F.34, V.36, A.37, F.40, F.41, G.95, V.98, S.99, L.102 Ligands: LDA.9 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.33, B:A.37 LDA.16: 18 residues within 4Å: Chain A: I.8, W.12, L.15, L.18, I.19, L.22 Chain B: W.151 Chain C: P.200, G.203, L.204, A.207, F.208, W.268, M.272, L.275 Ligands: LDA.1, BCL.5, UQ7.11 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:F.208, A:W.12 LDA.17: 14 residues within 4Å: Chain C: G.143, K.144, H.145, W.148, A.149, L.151, S.152, R.267, I.270, W.271, V.274, L.278 Ligands: LDA.3, PO4.18 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.148 Hydrogen bonds: C:K.144 LDA.21: 8 residues within 4Å: Chain B: P.28, F.29 Chain C: M.256, G.257, F.258 Ligands: LDA.1, BCL.6, UQ7.11 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.29

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.4: 39 residues within 4Å: Chain B: T.38, F.41, A.42, G.45, I.46, I.49, I.89, C.92, 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, F.180, S.237, L.238, V.241 Chain C: Y.210, A.213, L.214, A.217, M.218, W.252, T.255, M.256 Ligands: BCL.5, BCL.6, UQ7.11 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:I.49, B:A.93, B:A.120, B:F.121, B:F.121, B:F.123, B:A.124, B:Y.148, B:Y.148, B:L.238, B:V.241, B:V.241, C:Y.210, C:A.213 Hydrogen bonds: B:W.100, B:E.104 pi-Stacking: B:F.121 BPH.14: 28 residues within 4Å: Chain B: F.181, A.184, L.185, A.188, L.189, F.216, L.219, V.220 Chain C: S.59, L.60, G.63, W.66, A.125, V.126, W.129, T.133, T.146, A.149, F.150, S.152, A.153, A.273, V.274, V.276, T.277 Ligands: OLC.7, BCL.12, BCL.13 10 PLIP interactions: 2 interactions with chain B, 8 interactions with chain C Hydrophobic interactions: B:A.184, B:L.189, C:A.125, C:W.129, C:A.149, C:F.150, C:F.150, C:F.150 Hydrogen bonds: C:W.129 pi-Stacking: C:F.150

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.5: 26 residues within 4Å: Chain B: I.46, I.49, F.97, Y.128, L.131, F.146, I.150, W.151, H.153, L.154, W.156, V.157 Chain C: H.197, G.203, I.206, A.207, Y.210, G.211, L.214, M.272 Ligands: LDA.1, BPH.4, BCL.6, UQ7.11, BCL.12, LDA.16 11 PLIP interactions: 5 interactions with chain C, 6 interactions with chain B, Hydrophobic interactions: C:I.206, C:I.206, C:Y.210, C:L.214, B:I.49, B:Y.128, B:L.131, B:F.146, B:L.154 pi-Stacking: C:Y.210 Metal complexes: B:H.153 BCL.6: 37 residues within 4Å: Chain B: F.97, F.121, A.124, I.125, A.127, Y.128, T.130, 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, F.181, V.241, S.244, A.245, C.247, M.248 Chain C: T.186, H.197, L.209, Y.210 Ligands: BPH.4, BCL.5, UQ7.11, BCL.12, BCL.13, LDA.21 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:F.97, B:F.97, B:A.124, B:I.125, 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:Y.210 Hydrogen bonds: B:H.168 Metal complexes: B:H.173 BCL.12: 36 residues within 4Å: Chain B: V.157, Y.162, H.168, F.181 Chain C: W.66, M.122, V.126, F.150, A.153, I.154, L.156, W.157, L.160, W.185, T.186, N.187, F.189, S.190, N.195, L.196, H.197, F.201, H.202, S.205, I.206, L.209, Y.210, V.276, T.277, G.280, G.283, I.284 Ligands: BCL.5, BCL.6, BCL.13, BPH.14 14 PLIP interactions: 14 interactions with chain C, Hydrophobic interactions: C:W.66, C:A.153, C:L.156, C:W.157, C:T.186, C:N.187, C:F.189, C:L.196, C:I.206, C:L.209, C:Y.210, C:V.276 Hydrogen bonds: C:H.197 Metal complexes: C:H.202 BCL.13: 25 residues within 4Å: Chain B: H.168, M.174, I.177, T.178, F.181, T.182, L.185 Chain C: W.66, M.122, L.156, W.157, L.160, V.175, I.179, F.180, H.182, L.183, W.185, T.186 Ligands: BCL.6, OLC.7, BCL.12, BPH.14, OLC.19, SPN.20 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain B, Hydrophobic interactions: C:L.160, C:V.175, C:L.183, C:W.185, C:T.186, B:I.177, B:I.177, B:L.185 Metal complexes: C:H.182

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

OLC.7: 23 residues within 4Å: Chain B: T.182, L.185, A.186, L.189, H.190, L.193, P.209, 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.39, L.47 Ligands: BCL.13, BPH.14 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.216, B:F.216, B:V.220, B:Y.222, B:I.229 Hydrogen bonds: B:I.224, B:G.225 Water bridges: B:S.223 Salt bridges: B:H.190 OLC.19: 24 residues within 4Å: Chain C: W.66, F.67, F.68, I.70, G.71, I.72, F.74, W.75, F.85, L.89, W.115, M.122, W.157, L.160, G.161, A.174, V.175, P.176, Y.177, G.178, I.179, H.182 Ligands: BCL.13, SPN.20 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.67, C:F.67, C:F.67, C:I.70 Hydrogen bonds: C:W.157, C:V.175

1 x UQ7: UBIQUINONE-7(Non-covalent)

UQ7.11: 36 residues within 4Å: Chain B: V.26, F.29, Y.30, V.31, G.35, V.36, T.38, F.39, W.100, R.103 Chain C: L.214, L.215, M.218, H.219, T.222, I.223, A.245, A.248, A.249, W.252, T.255, M.256, F.258, N.259, A.260, T.261, M.262, I.265, W.268, M.272 Ligands: LDA.1, BPH.4, BCL.5, BCL.6, LDA.16, LDA.21 15 PLIP interactions: 11 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:M.218, C:W.252, C:M.256, C:F.258, C:A.260, C:I.265, C:I.265, C:W.268, C:W.268, B:F.29, B:F.29, B:W.100, B:W.100 Hydrogen bonds: C:H.219, C:A.260

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

FE.15: 7 residues within 4Å: Chain B: H.190, V.194, H.230 Chain C: H.219, I.223, 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

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

PO4.18: 5 residues within 4Å: Chain B: L.195, N.199 Chain C: H.145, R.267 Ligands: LDA.17 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Salt bridges: C:H.145, C:R.267 Hydrogen bonds: B:N.199 PO4.22: 5 residues within 4Å: Chain C: Y.3, Q.4, N.5, I.6, F.7 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.4, C:N.5, C:I.6, C:F.7, C:F.7

1 x SPN: SPEROIDENONE(Non-covalent)

SPN.20: 31 residues within 4Å: Chain C: W.66, F.67, F.68, I.70, G.71, I.72, F.74, W.75, F.85, L.89, F.105, W.115, L.116, S.119, F.120, M.122, F.123, W.157, M.158, G.161, F.162, W.171, A.174, V.175, P.176, Y.177, G.178, I.179, H.182 Ligands: BCL.13, OLC.19 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:F.67, C:F.67, C:F.68, C:I.70, C:W.115, C:F.120, C:F.120, C:F.123, C:F.162, C:F.162, C:F.162, C:W.171, C:Y.177, C:I.179, C:H.182 Hydrogen bonds: C:W.75

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.23: 10 residues within 4Å: Chain C: N.25, N.28, Y.51, G.53, S.54, L.55, G.56, L.135, R.136 Ligands: CL.24 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:Y.51 Hydrogen bonds: C:Y.51, C:S.54, C:S.54, C:L.55, C:R.136 Salt bridges: C:R.136

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

CL.24: 6 residues within 4Å: Chain C: Y.51, G.53, L.55, G.56, R.132 Ligands: CIT.23 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lieske, J. et al., Fixed-target high-pressure macromolecular crystallography. To Be Published

Release Date

2022-11-16

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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