SMTL ID : 7mha.1

Crystal structure of R. sphaeroides Photosynthetic Reaction Center variant; W252V mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.79 Å

Oligo State

hetero-1-1-1-mer

Ligands

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.1: 17 residues within 4Å: Chain B: Y.129, L.132, F.147, I.151, H.154, L.155, V.158 Chain C: F.198, G.204, I.207, A.208, Y.211, G.212 Ligands: BPH.2, BCL.4, BCL.8, LDA.9 12 PLIP interactions: 7 interactions with chain B, 5 interactions with chain C, Hydrophobic interactions: B:Y.129, B:L.132, B:F.147, B:F.147, B:L.155, B:V.158, C:F.198, C:I.207, C:I.207 Metal complexes: B:H.154 Water bridges: C:G.204 pi-Stacking: C:Y.211 BCL.4: 27 residues within 4Å: Chain B: F.98, A.125, I.126, A.128, Y.129, L.132, W.157, V.158, T.161, G.162, Y.163, N.167, F.168, H.169, H.174, A.177, I.178, F.181, S.245, A.246, C.248, M.249 Chain C: Y.211 Ligands: BCL.1, BPH.2, BCL.7, BCL.8 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:F.98, B:A.128, B:T.161, B:Y.163, B:F.168, B:A.177, B:I.178, B:F.181, B:F.181, C:Y.211 Hydrogen bonds: B:S.245 Metal complexes: B:H.174 BCL.7: 16 residues within 4Å: Chain B: H.169, M.175, I.178, S.179, T.183 Chain C: M.123, W.158, L.161, I.180, H.183, L.184, T.187 Ligands: BCL.4, BPH.5, BCL.8, SPO.13 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B, Hydrophobic interactions: C:L.161, C:L.184, B:I.178, B:I.178 Metal complexes: C:H.183 Hydrogen bonds: B:T.183 BCL.8: 25 residues within 4Å: Chain B: V.158, Y.163, F.182 Chain C: M.123, A.154, L.157, W.158, L.161, T.187, N.188, F.190, S.191, L.197, F.198, H.203, S.206, I.207, Y.211, V.277, G.281, I.285 Ligands: BCL.1, BCL.4, BPH.5, BCL.7 12 PLIP interactions: 1 interactions with chain B, 11 interactions with chain C, Hydrophobic interactions: B:V.158, C:L.157, C:W.158, C:T.187, C:N.188, C:F.190, C:L.197, C:F.198, C:I.207, C:Y.211, C:V.277 Metal complexes: C:H.203

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.2: 25 residues within 4Å: Chain B: F.42, A.43, I.50, A.94, A.97, F.98, W.101, E.105, I.118, A.121, F.122, A.125, Y.149, G.150, H.154, V.242 Chain C: Y.211, A.214, L.215, A.218, M.219, T.256, M.257 Ligands: BCL.1, BCL.4 16 PLIP interactions: 13 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:A.43, B:I.50, B:A.94, B:A.97, B:A.121, B:F.122, B:F.122, B:F.122, B:A.125, B:Y.149, B:Y.149, B:V.242, B:V.242, C:Y.211, C:A.214, C:A.218 BPH.5: 21 residues within 4Å: Chain B: F.182, A.185, L.186, A.189, L.190, L.220 Chain C: L.61, G.64, L.65, A.126, V.127, W.130, T.147, A.150, F.151, A.154, A.274, V.275, T.278 Ligands: BCL.7, BCL.8 13 PLIP interactions: 9 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:L.61, C:L.65, C:A.150, C:F.151, C:F.151, C:A.154, C:A.274, C:T.278, B:F.182, B:A.185, B:A.189, B:L.190 pi-Stacking: C:F.151

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

U10.3: 12 residues within 4Å: Chain B: L.190, H.191, L.194, E.213, D.214, F.217, Y.223, S.224, I.225, G.226, T.227, I.230 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.190, B:L.194, B:F.217, B:F.217, B:F.217, B:Y.223, B:I.225, B:I.230 Hydrogen bonds: B:D.214, B:I.225, B:G.226

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

CL.6: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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

LDA.9: 6 residues within 4Å: Chain C: P.201, G.204, L.205, A.208, W.269 Ligands: BCL.1 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:A.208, C:W.269 LDA.10: 4 residues within 4Å: Chain C: F.8, L.39, W.42, F.43 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.8, C:F.43 pi-Cation interactions: C:W.42 LDA.11: 3 residues within 4Å: Chain B: V.221 Chain C: G.32, G.34 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.32

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

FE.12: 5 residues within 4Å: Chain B: H.191, H.231 Chain C: H.220, E.235, H.267 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Metal complexes: B:H.191, B:H.231, C:H.220, C:E.235, C:H.267

1 x SPO: SPHEROIDENE(Non-covalent)

SPO.13: 19 residues within 4Å: Chain C: F.68, I.71, G.72, W.76, F.86, W.116, S.120, M.123, W.158, L.161, G.162, F.163, W.172, V.176, Y.178, G.179, I.180, H.183 Ligands: BCL.7 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:F.68, C:F.68, C:I.71, C:W.116, C:W.158, C:L.161, C:F.163, C:W.172, C:V.176, C:Y.178, C:I.180

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.14: 14 residues within 4Å: Chain A: A.16, S.19, F.23, G.26, L.27, Y.30 Chain B: N.200, P.201 Chain C: G.144, K.145, H.146, W.149, R.268, W.272 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:W.149, C:W.149, C:W.149, C:W.272, C:W.272, A:F.23, A:Y.30 Hydrogen bonds: C:K.145 Water bridges: C:K.145 Salt bridges: C:H.146, C:H.146, C:H.146, C:R.268

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Weaver, J.B. et al., Photosynthetic reaction center variants made via genetic code expansion indicate tyrosine at M210 tunes the mechanism for primary electron transfer. Thesis Ph.D. Stanford University (2022)

Release Date

2022-04-27

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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