SMTL ID : 8vtj.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.81 Å

Oligo State

hetero-1-1-1-mer

Ligands

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.1: 15 residues within 4Å: Chain B: I.46, Y.128, I.150, H.153, L.154 Chain C: F.196, G.202, I.205, A.206, X.209, G.210 Ligands: BPH.2, BCL.4, BCL.6, LDA.7 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain B, Hydrophobic interactions: C:F.196, C:I.205, C:I.205, B:I.46, B:Y.128, B:L.154 Metal complexes: B:H.153 BCL.4: 28 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: X.209 Ligands: BCL.1, BPH.2, BCL.6, BCL.14 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:F.97, B:A.124, B:V.157, B:T.160, B:Y.162, B:F.167, B:A.176, B:I.177, B:F.180, B:F.180 Hydrogen bonds: B:S.244 Metal complexes: B:H.173 BCL.6: 27 residues within 4Å: Chain B: V.157, Y.162, H.168, F.181 Chain C: M.121, 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.1, BCL.4, BPH.11, BCL.14 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain B, Hydrophobic interactions: C:A.152, C:L.155, C:W.156, C:T.185, C:N.186, C:F.188, C:L.195, C:F.196, C:I.205, C:I.205, C:L.208, C:V.275, B:V.157 Metal complexes: C:H.201 BCL.14: 16 residues within 4Å: Chain B: H.168, M.174, I.177, S.178, T.182 Chain C: M.121, W.156, I.178, H.181, L.182, W.184, T.185 Ligands: BCL.4, BCL.6, BPH.11, SPO.12 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain C, Hydrophobic interactions: B:I.177, B:I.177, C:L.182, C:W.184 pi-Stacking: B:F.181 Metal complexes: C:H.181

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.2: 25 residues within 4Å: Chain B: F.41, A.42, I.49, A.93, A.96, F.97, W.100, E.104, I.117, A.120, F.121, A.124, Y.148, G.149, I.150, H.153, V.241 Chain C: X.209, A.212, L.213, M.217, T.254, M.255 Ligands: BCL.1, BCL.4 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:I.49, B:W.100, B:A.120, B:F.121, B:F.121, B:F.121, B:Y.148, B:V.241, B:V.241, C:A.212 Hydrogen bonds: B:E.104 BPH.11: 24 residues within 4Å: Chain B: F.181, A.184, L.185, A.188, L.189, L.219, V.220 Chain C: S.58, L.59, G.62, L.63, F.66, A.124, V.125, W.128, T.132, T.145, A.148, F.149, A.152, A.272, T.276 Ligands: BCL.6, BCL.14 12 PLIP interactions: 10 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:L.63, C:F.66, C:W.128, C:W.128, C:F.149, C:F.149, C:F.149, C:F.149, C:A.152, C:T.276, B:F.181, B:A.184

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

U10.3: 7 residues within 4Å: Chain B: L.189, F.216, V.220, Y.222, I.224, L.232 Ligands: LDA.9 No protein-ligand interaction detected (PLIP)

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

CL.5: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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

LDA.7: 5 residues within 4Å: Chain A: W.21 Chain C: P.199, L.203, W.267 Ligands: BCL.1 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.267 LDA.8: 2 residues within 4Å: Chain C: F.6, W.40 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:W.40 pi-Cation interactions: C:W.40, C:W.40 LDA.9: 7 residues within 4Å: Chain B: V.220, G.221 Chain C: S.29, G.30, V.31, G.32 Ligands: U10.3 No protein-ligand interaction detected (PLIP)

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

FE.10: 5 residues within 4Å: Chain B: H.190, H.230 Chain C: H.218, E.233, H.265 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Metal complexes: B:H.190, B:H.230, C:H.218, C:E.233, C:H.265

1 x SPO: SPHEROIDENE(Non-covalent)

SPO.12: 21 residues within 4Å: Chain C: F.66, I.69, G.70, F.73, W.74, F.84, W.114, S.118, F.119, M.121, W.156, L.159, G.160, F.161, W.170, V.174, Y.176, G.177, I.178, H.181 Ligands: BCL.14 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:F.66, C:F.66, C:I.69, C:F.73, C:F.84, C:W.114, C:W.156, C:L.159, C:F.161, C:W.170, C:V.174, C:Y.176, C:I.178

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.13: 14 residues within 4Å: Chain A: A.16, S.19, L.27, Y.30 Chain B: N.199, P.200 Chain C: G.142, K.143, H.144, W.147, R.266, I.269, W.270, L.277 13 PLIP interactions: 10 interactions with chain C, 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: C:W.147, C:W.147, C:I.269, C:W.270, C:L.277, A:L.27, A:Y.30 Hydrogen bonds: C:K.143, B:N.199 Salt bridges: C:H.144, C:H.144, C:H.144, C:R.266

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mathews, I. et al., Crystal structure of R. sphaeroides Photosynthetic Reaction Center variant Y(M210)2-cyanophenylalanine. To Be Published

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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