- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.10 Å
- Oligo State
- hetero-1-1-1-mer
- Ligands
- 4 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)
- 4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)
BCL.2: 22 residues within 4Å:- Chain B: H.168, M.174, I.177, T.178, F.181, T.182, L.185
- Chain C: W.66, F.67, M.122, W.157, L.160, V.175, I.179, H.182, L.183, W.185, T.186
- Ligands: BCL.3, BCL.8, BPH.10, SPN.13
12 PLIP interactions:8 interactions with chain C, 4 interactions with chain B,- Hydrophobic interactions: C:W.66, C:F.67, C:F.67, C:L.160, C:V.175, C:L.183, C:W.185, B:I.177, B:I.177, B:L.185
- Metal complexes: C:H.182
- pi-Stacking: B:F.181
BCL.3: 29 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: Y.210
- Ligands: BCL.2, BPH.4, BCL.8, BCL.9, U10.12
14 PLIP interactions:13 interactions with chain B, 1 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:A.176, B:I.177, B:F.180, B:F.180, C:Y.210
- Hydrogen bonds: B:S.244
- Metal complexes: B:H.173
BCL.8: 26 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, G.280, I.284
- Ligands: BCL.2, BCL.3, BCL.9, BPH.10
14 PLIP interactions:14 interactions with chain C,- Hydrophobic interactions: C:A.153, C:L.156, C:W.157, C:T.186, C:F.189, C:L.196, C:F.197, C:F.197, C:I.206, C:L.209, C:Y.210, C:V.276, C:I.284
- Metal complexes: C:H.202
BCL.9: 23 residues within 4Å:- Chain B: I.46, I.49, Y.128, L.131, F.146, I.150, W.151, 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: BCL.3, BPH.4, BCL.8, U10.12, LDA.14
15 PLIP interactions:9 interactions with chain B, 6 interactions with chain C,- Hydrophobic interactions: B:I.46, 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:Y.210, C:L.214
- Metal complexes: B:H.153
- pi-Stacking: C:Y.210
- 2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)
BPH.4: 31 residues within 4Å:- Chain B: F.41, A.42, I.49, C.92, 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, M.218, W.252, T.255, M.256
- Ligands: BCL.3, BCL.9, U10.12
20 PLIP interactions:17 interactions with chain B, 3 interactions with chain C- Hydrophobic interactions: B:A.42, B:I.49, B:A.93, 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:Y.148, B:L.238, B:V.241, B:V.241, C:Y.210, C:A.213, C:L.214
- Hydrogen bonds: B:E.104
BPH.10: 27 residues within 4Å:- Chain B: F.181, A.184, L.185, A.188, L.189, F.216, L.219, V.220
- Chain C: S.59, G.63, L.64, W.66, F.67, F.68, A.125, V.126, W.129, T.133, T.146, A.149, F.150, A.153, A.273, V.274, T.277
- Ligands: BCL.2, BCL.8
16 PLIP interactions:12 interactions with chain C, 4 interactions with chain B- Hydrophobic interactions: C:W.66, C:F.67, C:F.67, C:F.68, C:W.129, C:W.129, C:A.149, C:F.150, C:F.150, C:A.153, C:T.277, B:A.184, B:L.185, B:A.188, B:L.189
- pi-Stacking: C:F.150
- 5 x UNL: UNKNOWN LIGAND
UNL.5: 7 residues within 4Å:- Chain B: L.75, G.77, Q.87, T.90, I.91, T.94, W.142
4 PLIP interactions:4 interactions with chain B- Hydrophobic interactions: B:Q.87, B:I.91, B:T.94, B:W.142
UNL.6: 5 residues within 4Å:- Chain B: A.101, L.102, V.105, A.122
- Ligands: UNL.19
5 PLIP interactions:5 interactions with chain B- Hydrophobic interactions: B:A.101, B:L.102, B:V.105, B:V.105, B:A.122
UNL.17: 5 residues within 4Å:- Chain B: P.28, F.29
- Chain C: M.256, G.257
- Ligands: LDA.1
2 PLIP interactions:2 interactions with chain B- Hydrophobic interactions: B:P.28, B:F.29
UNL.18: 5 residues within 4Å:- Chain A: L.3
- Chain C: L.167, L.285, T.289, V.290
2 PLIP interactions:1 interactions with chain C, 1 interactions with chain A- Hydrophobic interactions: C:V.290, A:L.3
UNL.19: 5 residues within 4Å:- Chain B: F.119
- Chain C: Q.4, I.6
- Ligands: UNL.6, PO4.20
3 PLIP interactions:2 interactions with chain C, 1 interactions with chain B- Hydrophobic interactions: C:Q.4, C:I.6, B:F.119
- 1 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)
OLC.7: 13 residues within 4Å:- Chain B: H.190, L.193, E.212, D.213, F.216, V.220, G.221, Y.222, S.223, I.224, G.225, T.226, I.229
11 PLIP interactions:11 interactions with chain B- Hydrophobic interactions: B:F.216, B:F.216, B:F.216, B:V.220, B:Y.222, B:I.229
- Hydrogen bonds: B:E.212, B:S.223, B:I.224, B:G.225
- Salt bridges: B:H.190
- 1 x FE: FE (III) ION(Non-covalent)
- 1 x U10: UBIQUINONE-10(Non-covalent)
U10.12: 27 residues within 4Å:- Chain B: V.26, F.29, G.35, T.38, 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, M.262, I.265, W.268, M.272
- Ligands: LDA.1, BCL.3, BPH.4, BCL.9
20 PLIP interactions:6 interactions with chain B, 14 interactions with chain C- Hydrophobic interactions: B:V.26, B:F.29, B:F.29, B:T.38, B:W.100, B:W.100, C:L.214, C:M.218, C:H.219, C:W.252, C:M.256, C:F.258, C:F.258, C:A.260, C:I.265, C:I.265, C:W.268, C:W.268
- Hydrogen bonds: C:T.222, C:A.260
- 1 x SPN: SPEROIDENONE(Non-covalent)
SPN.13: 22 residues within 4Å:- Chain C: F.67, F.68, I.70, G.71, F.74, W.75, L.89, W.115, S.119, F.120, M.122, W.157, L.160, G.161, F.162, W.171, V.175, Y.177, G.178, I.179, H.182
- Ligands: BCL.2
18 PLIP interactions:18 interactions with chain C- Hydrophobic interactions: C:F.67, C:F.67, C:I.70, C:I.70, C:F.74, C:F.74, C:L.89, C:W.115, C:F.120, C:W.157, C:L.160, C:F.162, C:F.162, C:F.162, C:W.171, C:V.175, C:V.175, C:I.179
- 1 x PO4: PHOSPHATE ION(Non-functional Binders)
- 2 x NKP: (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate(Non-covalent)
NKP.21: 11 residues within 4Å:- Chain C: G.143, K.144, H.145, W.148, L.151, W.155, W.271, V.274, L.278, I.282
- Ligands: NKP.22
14 PLIP interactions:14 interactions with chain C- Hydrophobic interactions: C:W.148, C:L.151, C:L.151, C:W.155, C:W.271, C:V.274, C:L.278, C:I.282
- Hydrogen bonds: C:K.144
- Water bridges: C:K.144, C:K.144, C:R.267
- Salt bridges: C:H.145, C:H.145
NKP.22: 10 residues within 4Å:- Chain A: I.13, F.14, A.16, G.17, L.18, Y.21
- Chain B: N.199
- Chain C: H.145, R.267
- Ligands: NKP.21
10 PLIP interactions:7 interactions with chain A, 2 interactions with chain C, 1 interactions with chain B- Hydrophobic interactions: A:I.13, A:F.14, A:A.16, A:L.18, A:Y.21, A:Y.21
- Hydrogen bonds: A:Y.21, B:N.199
- Salt bridges: C:H.145, C:R.267
- 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
HB
LC
M - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.10 Å
- Oligo State
- hetero-1-1-1-mer
- Ligands
- 4 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)
- 4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)
- 2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)
- 5 x UNL: UNKNOWN LIGAND
- 1 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)
- 1 x FE: FE (III) ION(Non-covalent)
- 1 x U10: UBIQUINONE-10(Non-covalent)
- 1 x SPN: SPEROIDENONE(Non-covalent)
- 1 x PO4: PHOSPHATE ION(Non-functional Binders)
- 2 x NKP: (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate(Non-covalent)
- 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
HB
LC
M - Membrane
-
We predict this structure to be a membrane protein.