SMTL ID : 6z27.1

Photosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV LCP crystallization

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

LDA.1: 8 residues within 4Å: Chain A: W.21 Chain C: P.200, A.207, F.208, W.268, M.272 Ligands: LDA.2, BCL.14 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:W.21, A:W.21, C:A.207, C:W.268 LDA.2: 10 residues within 4Å: Chain A: Q.32, Y.40, L.42, Q.53, F.56 Chain C: R.253, F.258 Ligands: LDA.1, U10.17, LDA.20 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:F.258, C:F.258, C:F.258, A:F.56 Hydrogen bonds: C:R.253, C:R.253 LDA.7: 7 residues within 4Å: Chain B: A.78, G.84, Q.87, I.88, T.90, T.94, W.142 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.142, B:W.142 LDA.11: 6 residues within 4Å: Chain A: L.12 Chain C: L.167, G.288, T.289, V.290, D.292 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:L.167, A:L.12 Hydrogen bonds: C:D.292 Salt bridges: C:D.292 LDA.18: 5 residues within 4Å: Chain B: L.235 Chain C: F.7, L.38, W.41, F.42 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:F.7, C:F.7, C:L.38, C:W.41, C:F.42, C:F.42, C:F.42, B:L.235 pi-Cation interactions: C:W.41, C:W.41 LDA.19: 7 residues within 4Å: Chain B: V.220, G.221 Chain C: S.30, G.31, V.32, G.33, G.48 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.31 LDA.20: 7 residues within 4Å: Chain B: P.28, F.29 Chain C: M.256, G.257 Ligands: LDA.2, BCL.14, U10.17 No protein-ligand interaction detected (PLIP)

8 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 4 residues within 4Å: Chain A: G.127, H.128, N.129, K.132 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.129 Salt bridges: A:H.128, A:K.132 PO4.4: 3 residues within 4Å: Chain A: H.141, V.142, N.147 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.142, A:N.147 PO4.5: 2 residues within 4Å: Chain A: G.71, T.72 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.72 Water bridges: A:T.72 PO4.21: 4 residues within 4Å: Chain B: N.199 Chain C: H.145, R.267 Ligands: PO4.24 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Salt bridges: C:H.145, C:R.267 Water bridges: A:K.62 Hydrogen bonds: B:N.199 PO4.22: 5 residues within 4Å: Chain C: N.25, N.28, Y.51, G.53, S.54 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.25, C:N.28, C:Y.51, C:S.54 PO4.23: 4 residues within 4Å: Chain C: F.35, S.36, T.37, L.38 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:F.35, C:S.36, C:T.37, C:L.38 PO4.24: 4 residues within 4Å: Chain C: G.143, K.144, H.145 Ligands: PO4.21 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.144 Water bridges: C:K.144 Salt bridges: C:K.144, C:H.145 PO4.25: 5 residues within 4Å: Chain C: Y.3, Q.4, N.5, I.6, F.7 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.4, C:I.6, C:F.7, C:F.7

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

OLC.6: 13 residues within 4Å: Chain B: L.185, L.189, H.190, L.193, D.213, F.216, S.223, I.224, G.225, T.226, I.229 Ligands: BCL.13, BPH.15 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.185, B:L.189, B:F.216, B:I.229, B:I.229 Hydrogen bonds: B:D.213, B:S.223, B:I.224, B:G.225 Water bridges: B:P.209, B:D.213 Salt bridges: B:H.190 OLC.10: 15 residues within 4Å: Chain C: F.67, G.71, W.75, L.89, W.115, M.122, W.157, G.161, F.162, A.174, V.175, Y.177, G.178, H.182 Ligands: BCL.12 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.67, C:F.67, C:F.67, C:L.89, C:V.175, C:H.182 Hydrogen bonds: C:V.175, C:Y.177

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.8: 29 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, Y.162, F.167, H.168, H.173, A.176, I.177, F.180, F.181, S.244, A.245, C.247, M.248 Chain C: F.197, Y.210 Ligands: BPH.9, BCL.12, BCL.13, BCL.14, U10.17 18 PLIP interactions: 15 interactions with chain B, 3 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:F.167, B:A.176, B:I.177, B:F.180, B:F.180, B:F.181, C:F.197, C:F.197, C:Y.210 Hydrogen bonds: B:S.244 Metal complexes: B:H.173 BCL.12: 21 residues within 4Å: Chain B: H.168, M.174, I.177, T.178, F.181, T.182, L.185 Chain C: W.66, L.89, M.122, W.157, L.160, V.175, I.179, H.182, L.183, T.186 Ligands: BCL.8, OLC.10, BCL.13, BPH.15 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain B, Hydrophobic interactions: C:W.66, C:L.89, C:L.160, C:V.175, C:I.179, C:L.183, B:I.177, B:I.177, B:L.185 Metal complexes: C:H.182 BCL.13: 28 residues within 4Å: Chain B: V.157, Y.162, H.168, F.181 Chain C: A.153, L.156, W.157, L.160, T.186, N.187, F.189, S.190, L.196, F.197, H.202, S.205, I.206, L.209, Y.210, V.276, T.277, G.280, I.284 Ligands: OLC.6, BCL.8, BCL.12, BCL.14, BPH.15 14 PLIP interactions: 14 interactions with chain C, Hydrophobic interactions: C:A.153, C:L.156, C:W.157, C:T.186, C:N.187, C:F.189, C:L.196, C:F.197, C:F.197, C:I.206, C:L.209, C:Y.210, C:V.276 Metal complexes: C:H.202 BCL.14: 22 residues within 4Å: Chain B: I.49, Y.128, L.131, F.146, I.150, H.153, L.154, W.156, V.157 Chain C: F.197, G.203, I.206, A.207, Y.210, G.211, L.214 Ligands: LDA.1, BCL.8, BPH.9, BCL.13, U10.17, LDA.20 15 PLIP interactions: 8 interactions with chain B, 7 interactions with chain C, Hydrophobic interactions: B:I.49, B:Y.128, B:L.131, B:F.146, B:L.154, B:W.156, B:V.157, C:F.197, C:I.206, C:I.206, C:A.207, C:Y.210, C:L.214 Metal complexes: B:H.153 pi-Stacking: C:Y.210

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.9: 31 residues within 4Å: Chain B: T.38, F.41, 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, A.217, M.218, W.252, T.255, M.256 Ligands: BCL.8, BCL.14, U10.17 18 PLIP interactions: 4 interactions with chain C, 14 interactions with chain B Hydrophobic interactions: C:Y.210, C:A.213, C:L.214, C:A.217, B:I.49, 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:L.238, B:V.241, B:V.241 Hydrogen bonds: B:E.104 BPH.15: 26 residues within 4Å: Chain B: F.181, L.185, A.188, L.189, L.219, V.220 Chain C: S.59, L.60, G.63, L.64, W.66, F.67, A.125, V.126, W.129, T.133, T.146, A.149, F.150, A.153, A.273, V.274, T.277 Ligands: OLC.6, BCL.12, BCL.13 15 PLIP interactions: 13 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:L.60, C:L.64, C:W.66, C:F.67, C:F.67, C:F.67, C:W.129, C:A.149, C:F.150, C:F.150, C:F.150, C:F.150, C:A.153, B:A.188, B:L.189

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

FE.16: 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 U10: UBIQUINONE-10(Non-covalent)

U10.17: 28 residues within 4Å: Chain B: V.26, F.29, G.35, T.38, F.39, 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, I.265, W.268, M.272 Ligands: LDA.2, BCL.8, BPH.9, BCL.14, LDA.20 21 PLIP interactions: 12 interactions with chain C, 9 interactions with chain B Hydrophobic interactions: C:L.214, C:M.218, C:W.252, C:M.256, 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:F.29, B:T.38, B:F.39, B:W.100, B:W.100, B:W.100 Hydrogen bonds: C:T.222, C:A.260

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

EDO.26: 4 residues within 4Å: Chain A: H.126 Chain C: M.20, T.21, E.22 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:T.21, C:E.22, C:E.22, A:H.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Selikhanov, G. et al., Novel approaches for the lipid sponge phase crystallization of the Rhodobacter sphaeroides photosynthetic reaction center. Iucrj (2020)

Release Date

2020-12-02

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