SMTL ID : 8vtm.1

Crystal structure of R. sphaeroides Photosynthetic Reaction Center variant Y(M210)2-bromophenylalanine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.51 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

LDA.1: 7 residues within 4Å: Chain A: W.11, I.18 Chain C: L.203, A.206, F.207, M.271 Ligands: BCL.2 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:L.203, C:A.206, C:F.207, A:W.11, A:I.18 Hydrogen bonds: C:P.199 LDA.6: 3 residues within 4Å: Chain C: L.37, W.40, F.41 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.37, C:W.40, C:W.40, C:F.41 pi-Cation interactions: C:W.40 LDA.7: 5 residues within 4Å: Chain B: V.220, G.221 Chain C: S.29, G.30, I.49 No protein-ligand interaction detected (PLIP)

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)(Covalent)

BCL.2: 18 residues within 4Å: Chain B: I.46, I.49, Y.128, L.131, F.146, H.153, L.154 Chain C: F.196, G.202, I.205, A.206, X.209, G.210, L.213 Ligands: LDA.1, BCL.3, BCL.5, BPH.12 10 PLIP interactions: 3 interactions with chain C, 7 interactions with chain B, Hydrophobic interactions: C:F.196, C:I.205, C:L.213, B:I.46, B:I.49, B:Y.128, B:L.131, B:F.146, B:L.154 Metal complexes: B:H.153 BCL.3: 26 residues within 4Å: Chain B: F.97, A.124, I.125, A.127, L.131, W.156, V.157, S.158, T.160, G.161, N.166, F.167, H.168, H.173, A.176, I.177, F.180, S.244, A.245, C.247, M.248 Chain C: T.185 Ligands: BCL.2, BCL.5, BPH.12, BCL.13 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:F.97, B:F.97, B:F.97, B:A.127, B:W.156, B:V.157, B:T.160, B:F.167, B:F.167, B:A.176, B:I.177, B:F.180, C:T.185 Hydrogen bonds: B:S.244 Metal complexes: B:H.173 BCL.5: 26 residues within 4Å: Chain B: V.157, Y.162, H.168, F.181 Chain C: A.152, L.155, W.156, L.159, T.185, N.186, F.188, S.189, L.195, F.196, H.201, S.204, I.205, L.208, X.209, V.275, G.279, I.283 Ligands: BCL.2, BCL.3, BPH.9, BCL.13 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain B, Hydrophobic interactions: C:L.155, C:W.156, C:T.185, C:F.188, C:L.195, C:F.196, C:F.196, C:F.196, C:I.205, C:L.208, C:V.275, C:I.283, B:V.157 Hydrogen bonds: C:S.204 Metal complexes: C:H.201 BCL.13: 15 residues within 4Å: Chain B: H.168, M.174, I.177, S.178, T.182 Chain C: L.159, I.178, H.181, L.182, W.184, T.185 Ligands: BCL.3, BCL.5, BPH.9, SPO.10 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain B, Hydrophobic interactions: C:L.159, C:I.178, C:L.182, C:W.184, B:I.177, B:I.177 Metal complexes: C:H.181 pi-Stacking: B:F.181

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

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

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

FE.8: 5 residues within 4Å: Chain B: H.190, H.230 Chain C: H.218, E.233, H.265 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Metal complexes: C:H.218, C:E.233, C:E.233, B:H.190, B:H.230

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)(Covalent)

BPH.9: 20 residues within 4Å: Chain B: F.181, A.184, L.185, L.189, L.219 Chain C: S.58, G.62, L.63, F.66, A.124, V.125, W.128, T.145, A.148, F.149, A.152, A.272, T.276 Ligands: BCL.5, BCL.13 9 PLIP interactions: 2 interactions with chain B, 7 interactions with chain C Hydrophobic interactions: B:A.184, B:L.189, C:L.63, C:F.66, C:A.148, C:F.149, C:F.149, C:A.152, C:T.276 BPH.12: 24 residues within 4Å: Chain B: T.38, F.41, A.42, I.49, I.89, A.93, A.96, F.97, W.100, E.104, I.117, A.120, F.121, A.124, Y.148, V.241 Chain C: X.209, A.212, L.213, A.216, M.217, M.255 Ligands: BCL.2, BCL.3 15 PLIP interactions: 3 interactions with chain C, 12 interactions with chain B Hydrophobic interactions: C:A.212, C:L.213, C:A.216, B:A.42, B:I.49, B:I.89, B:F.97, B:F.97, B:F.121, B:A.124, B:Y.148, B:Y.148, B:V.241, B:V.241 pi-Stacking: B:F.121

1 x SPO: SPHEROIDENE(Covalent)

SPO.10: 18 residues within 4Å: Chain C: F.66, F.67, I.69, G.70, W.74, S.118, F.119, M.121, W.156, L.159, G.160, F.161, V.174, Y.176, G.177, I.178, H.181 Ligands: BCL.13 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:F.66, C:F.66, C:F.67, C:I.69, C:F.119, C:W.156, C:L.159, C:F.161, C:F.161, C:F.161, C:V.174, C:V.174, C:Y.176, C:I.178

1 x CDL: CARDIOLIPIN(Covalent)

CDL.11: 17 residues within 4Å: Chain A: S.9, F.10, F.13, G.16, L.17, Y.20 Chain B: N.199, P.200, K.202 Chain C: G.142, K.143, H.144, W.147, W.154, R.266, W.270, L.277 19 PLIP interactions: 4 interactions with chain A, 14 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: A:F.10, A:F.13, A:L.17, A:Y.20, C:W.147, C:W.147, C:W.154, C:W.270, C:W.270, C:L.277, C:L.277 Hydrogen bonds: C:K.143 Salt bridges: C:K.143, C:H.144, C:H.144, C:H.144, C:R.266, C:R.266, B:K.202

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tran, K.N. et al., Application of Amber Suppression To Study the Role of Tyr M210 in Electron Transfer in Rhodobacter sphaeroides Photosynthetic Reaction Centers. J.Phys.Chem.B (2025)

Release Date

2024-03-13

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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