SMTL ID : 7mh4.1

Crystal structure of R. sphaeroides Photosynthetic Reaction Center variant; Y(M210)3-bromotyrosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.48 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

LDA.1: 9 residues within 4Å: Chain A: Q.32, Y.40, L.42, Q.53, F.56 Chain C: R.254, F.259 Ligands: LDA.10, U10.15 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:Q.32, A:F.56, C:F.259 Hydrogen bonds: A:Y.40, A:Y.40, C:R.254, C:R.254 LDA.10: 8 residues within 4Å: Chain A: W.21 Chain C: P.201, G.204, L.205, A.208, W.269 Ligands: LDA.1, BCL.2 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:A.208, C:W.269 LDA.11: 5 residues within 4Å: Chain C: F.8, S.9, 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.12: 3 residues within 4Å: Chain B: P.29 Chain C: M.257, G.258 No protein-ligand interaction detected (PLIP) LDA.13: 4 residues within 4Å: Chain B: V.221, G.222 Chain C: G.32, G.34 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.32

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.2: 18 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, L.215 Ligands: BPH.3, BCL.5, BCL.9, LDA.10, U10.15 11 PLIP interactions: 7 interactions with chain B, 4 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, C:L.215 Metal complexes: B:H.154 BCL.5: 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.2, BPH.3, BCL.8, BCL.9 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:F.98, B:F.98, B:A.125, B:A.128, B:V.158, B:T.161, B:Y.163, B:F.168, B:A.177, B:I.178, B:F.181, B:F.181 Hydrogen bonds: B:S.245 Metal complexes: B:H.174 BCL.8: 16 residues within 4Å: Chain B: H.169, M.175, I.178, S.179, T.183, L.186 Chain C: M.123, W.158, I.180, H.183, L.184, T.187 Ligands: BCL.5, BPH.6, BCL.9, SPO.16 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain C, Hydrophobic interactions: B:I.178, B:I.178, B:L.186, C:L.184 Hydrogen bonds: B:T.183 pi-Stacking: B:F.182 Metal complexes: C:H.183 BCL.9: 27 residues within 4Å: Chain B: V.158, Y.163, H.169, 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, L.210, Y.211, V.277, G.281, I.285 Ligands: BCL.2, BCL.5, BPH.6, BCL.8 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain B, Hydrophobic interactions: C:A.154, C:L.157, C:W.158, C:T.187, C:F.190, C:L.197, C:F.198, C:I.207, C:L.210, C:V.277, B:V.158 Metal complexes: C:H.203

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.3: 26 residues within 4Å: Chain B: T.39, A.43, I.50, A.94, A.97, F.98, W.101, E.105, I.118, A.121, F.122, A.125, Y.149, H.154, S.238, L.239, V.242 Chain C: Y.211, A.214, L.215, A.218, W.253, T.256, M.257 Ligands: BCL.2, BCL.5 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:Y.149, B:Y.149, B:L.239, B:V.242, B:V.242, C:A.214, C:L.215, C:A.218 BPH.6: 18 residues within 4Å: Chain B: F.182, A.185, L.186, L.190, L.220 Chain C: G.64, A.126, V.127, W.130, T.147, A.150, F.151, A.154, A.274, V.275, T.278 Ligands: BCL.8, BCL.9 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:W.130, C:A.150, C:F.151, C:F.151, C:A.154, C:T.278, B:F.182, B:A.185 pi-Stacking: C:F.151

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

U10.4: 13 residues within 4Å: Chain B: L.190, H.191, L.194, V.195, E.213, D.214, F.217, Y.223, S.224, I.225, G.226, T.227, I.230 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.190, B:H.191, B:L.194, B:F.217, B:F.217, B:Y.223, B:I.225, B:I.230, B:I.230 Hydrogen bonds: B:D.214, B:I.225, B:G.226 U10.15: 22 residues within 4Å: Chain B: G.36, T.39, F.40, W.101, R.104 Chain C: M.219, H.220, T.223, A.249, A.250, W.253, M.257, F.259, N.260, A.261, T.262, M.263, I.266, W.269, M.273 Ligands: LDA.1, BCL.2 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:M.219, C:W.253, C:M.257, C:F.259, C:F.259, C:A.261, C:I.266, C:I.266, C:W.269, C:W.269, B:T.39, B:W.101 Hydrogen bonds: C:T.223, C:A.261

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

CL.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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

FE.14: 5 residues within 4Å: Chain B: H.191, H.231 Chain C: H.220, E.235, H.267 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Metal complexes: C:H.220, C:E.235, C:H.267, B:H.191, B:H.231

1 x SPO: SPHEROIDENE(Non-covalent)

SPO.16: 19 residues within 4Å: Chain C: F.68, F.69, I.71, G.72, W.76, F.86, W.116, S.120, M.123, W.158, L.161, G.162, W.172, V.176, Y.178, G.179, I.180, H.183 Ligands: BCL.8 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:F.68, C:F.68, C:F.69, C:I.71, C:W.116, C:W.158, C:L.161, C:W.172, C:V.176, C:V.176, C:Y.178, C:I.180

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.17: 14 residues within 4Å: Chain A: A.16, S.19, Y.30 Chain B: N.200, P.201, K.203 Chain C: G.144, K.145, H.146, W.149, W.156, R.268, W.272, I.283 17 PLIP interactions: 14 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:W.149, C:W.149, C:W.149, C:W.156, C:W.272, C:W.272, C:I.283, A:Y.30 Hydrogen bonds: C:K.145 Water bridges: C:K.145, C:R.268, A:K.62, A:K.62 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 show Tyr at M210 tunes the initial electron transfer mechanism. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-12-29

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.
Show / Hide

Reaction center protein H chain

Reaction center protein L chain

Reaction center protein M chain

Related Entries With Identical Sequence