SMTL ID : 7p0q.1

F(M197)H mutant structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV by fixed-target serial synchrotron crystallography (100K, 26keV)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

LDA.1: 9 residues within 4Å: Chain A: A.8, S.11, F.15 Chain C: W.148, W.271, L.278, I.282 Ligands: NKP.10, NKP.12 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:W.148, C:W.271, C:L.278, A:F.15, A:F.15 LDA.3: 11 residues within 4Å: Chain A: Q.24, Y.32, F.48 Chain C: R.253, G.257, F.258, W.268 Ligands: UNL.2, UNL.13, U10.14, UNL.15 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain C Water bridges: A:Q.24 Hydrophobic interactions: C:F.258, C:F.258, C:F.258, C:W.268 Hydrogen bonds: C:R.253, C:R.253 LDA.21: 6 residues within 4Å: Chain C: F.7, T.8, Q.9, L.38, W.41, F.42 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.7, C:L.38, C:W.41, C:F.42, C:F.42 Hydrogen bonds: C:Q.9 LDA.22: 7 residues within 4Å: Chain C: F.105, A.107, G.113, L.116, I.117, F.120, F.121 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.116, C:I.117, C:F.120, C:F.120, C:F.121

7 x UNL: UNKNOWN LIGAND

UNL.2: 7 residues within 4Å: Chain A: Y.10, W.13, I.14, A.17, I.20 Ligands: LDA.3, UNL.15 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.13, A:W.13, A:W.13, A:I.14, A:A.17, A:I.20 UNL.5: 6 residues within 4Å: Chain B: L.75, G.76, G.77, Q.87, T.90, W.142 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Q.87, B:W.142, B:W.142 UNL.9: 11 residues within 4Å: Chain B: V.98, A.101, L.102, V.105, Y.115, F.119, A.122, I.125, L.126, L.129 Ligands: UNL.11 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.98, B:A.101, B:L.102, B:V.105, B:Y.115, B:A.122, B:I.125, B:L.126, B:L.129 UNL.11: 3 residues within 4Å: Chain B: F.119 Chain C: Q.4 Ligands: UNL.9 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:Q.4, B:F.119, B:F.119, B:F.119 UNL.13: 7 residues within 4Å: Chain A: L.23 Chain C: A.207, F.208, W.271, M.272 Ligands: LDA.3, BCL.7 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:L.23, C:A.207, C:F.208, C:W.271 UNL.15: 8 residues within 4Å: Chain B: P.28, F.29 Chain C: M.256, G.257, F.258 Ligands: UNL.2, LDA.3, U10.14 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.258, B:P.28, B:F.29 UNL.23: 5 residues within 4Å: Chain A: L.4 Chain C: L.167, L.285, T.289, V.290 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:L.167, C:V.290, A:L.4

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

OLC.4: 15 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 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:L.189, B:F.216, B:F.216, B:V.220, B:Y.222, B:Y.222, B:I.229, B:L.232 Hydrogen bonds: B:E.212, B:S.223, B:I.224, B:G.225 Water bridges: B:D.213 Salt bridges: B:H.190

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.6: 29 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: Y.210 Ligands: BCL.7, BPH.8, U10.14, BCL.16, BCL.17 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:A.127, B:T.160, B:Y.162, B:F.167, B:A.176, B:I.177, B:I.177, B:F.180, B:F.180, C:Y.210 Hydrogen bonds: B:S.244 Metal complexes: B:H.173 BCL.7: 22 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: H.197, G.203, I.206, A.207, Y.210, G.211, L.214 Ligands: BCL.6, BPH.8, UNL.13, U10.14, BCL.17 14 PLIP interactions: 9 interactions with chain B, 5 interactions with chain C, Hydrophobic interactions: B:I.46, B:I.49, B:Y.128, B:L.131, B:F.146, B:L.154, B:L.154, B:V.157, C:I.206, C:I.206, C:Y.210, C:L.214 Metal complexes: B:H.153 pi-Stacking: C:Y.210 BCL.16: 19 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, I.179, H.182, L.183, T.186 Ligands: BCL.6, BCL.17, BPH.18, SPN.20 10 PLIP interactions: 5 interactions with chain C, 5 interactions with chain B, Hydrophobic interactions: C:W.66, C:F.67, C:F.67, C:L.183, B:I.177, B:I.177, B:T.182, B:L.185 Metal complexes: C:H.182 pi-Stacking: B:F.181 BCL.17: 29 residues within 4Å: Chain B: V.157, Y.162, H.168, F.181 Chain C: M.122, V.126, A.153, L.156, W.157, L.160, T.186, N.187, F.189, S.190, L.196, H.197, H.202, S.205, I.206, L.209, Y.210, V.276, T.277, G.280, I.284 Ligands: BCL.6, BCL.7, BCL.16, BPH.18 14 PLIP interactions: 14 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:L.196, C:I.206, C:L.209, C:Y.210, C:V.276, C:I.284 Metal complexes: C:H.202

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.8: 31 residues within 4Å: Chain B: 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, Y.148, G.149, I.150, H.153, L.238, V.241 Chain C: Y.210, A.213, L.214, M.218, W.252, T.255, M.256 Ligands: BCL.6, BCL.7, U10.14 20 PLIP interactions: 17 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:A.42, B:I.49, B:A.93, B:A.96, B:A.120, B:F.121, B:F.121, B:F.121, B:F.123, B:A.124, B:Y.128, B:Y.148, B:Y.148, B:L.238, B:V.241, B:V.241, C:Y.210, C:A.213, C:L.214 Hydrogen bonds: B:E.104 BPH.18: 25 residues within 4Å: Chain B: F.181, A.184, L.185, A.188, L.189, L.219 Chain C: S.59, G.63, L.64, W.66, F.67, F.68, A.125, V.126, W.129, T.133, T.146, A.149, F.150, A.153, A.273, V.274, T.277 Ligands: BCL.16, BCL.17 16 PLIP interactions: 12 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:W.66, C:F.67, C:F.67, C:F.68, 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:A.188, B:L.189

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

NKP.10: 11 residues within 4Å: Chain A: I.14, F.15, G.18, L.19, Y.21, Y.22 Chain B: N.199 Chain C: H.145, R.267 Ligands: LDA.1, NKP.12 12 PLIP interactions: 2 interactions with chain C, 9 interactions with chain A, 1 interactions with chain B Salt bridges: C:H.145, C:R.267 Hydrophobic interactions: A:F.15, A:F.15, A:Y.21, A:Y.22, A:Y.22 Hydrogen bonds: A:Y.22, B:N.199 Water bridges: A:E.26, A:R.29, A:K.54 NKP.12: 12 residues within 4Å: Chain C: G.143, K.144, H.145, W.148, L.151, W.155, I.270, W.271, V.274, L.278 Ligands: LDA.1, NKP.10 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:W.148, C:L.151, 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 Water bridges: C:K.144, C:R.267 Salt bridges: C:H.145, C:H.145

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

U10.14: 34 residues within 4Å: Chain B: V.26, F.29, Y.30, V.31, G.35, T.38, F.39, A.42, A.43, I.46, W.100, R.103 Chain C: 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: LDA.3, BCL.6, BCL.7, BPH.8, UNL.15 23 PLIP interactions: 13 interactions with chain C, 10 interactions with chain B Hydrophobic interactions: C:L.214, C:M.218, C:W.252, C:M.256, C:F.258, C:F.258, C:A.260, C:I.265, C:I.265, C:W.268, C:W.268, B:V.26, B:F.29, B:F.29, B:V.31, B:T.38, B:F.39, B:A.42, B:I.46, B:W.100, B:W.100 Hydrogen bonds: C:T.222, C:A.260

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

FE.19: 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 SPN: SPEROIDENONE(Non-covalent)

SPN.20: 24 residues within 4Å: Chain C: F.67, F.68, I.70, G.71, F.74, W.75, F.85, L.89, W.115, 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.16 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:F.67, C:F.67, C:F.67, C:F.68, C:I.70, C:I.70, C:F.74, C:F.85, C:L.89, C:W.115, C:F.123, C:W.157, C:L.160, C:F.162, C:F.162, C:F.162, C:W.171, C:V.175, C:I.179

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

EDO.24: 4 residues within 4Å: Chain A: H.118 Chain C: M.20, T.21, E.22 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.21, C:E.22, C:E.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gabdulkhakov, A.G. et al., X-Ray structure of Rhodobacter sphaeroides reaction center with M197 Phe-His substitution clarifies properties of the mutant complex. To Be Published

Release Date

2022-07-13

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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