- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.04 Å
- Oligo State
- hetero-1-1-1-mer
- Ligands
- 2 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)
- 1 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)
OLC.2: 15 residues within 4Å:- Chain B: L.189, 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, L.232
11 PLIP interactions:11 interactions with chain B- Hydrophobic interactions: B:L.189, B:F.216, B:Y.222, B:Y.222, B:I.229, B:L.232
- Hydrogen bonds: B:E.212, B:S.223, B:I.224, B:G.225
- Salt bridges: B:H.190
- 3 x MYS: PENTADECANE(Non-covalent)
MYS.3: 3 residues within 4Å:- Chain B: G.77, Q.87, W.142
2 PLIP interactions:2 interactions with chain B- Hydrophobic interactions: B:Q.87, B:W.142
MYS.4: 6 residues within 4Å:- Chain B: V.98, A.101, Y.115, P.118, I.125
- Chain C: Q.4
6 PLIP interactions:5 interactions with chain B, 1 interactions with chain C- Hydrophobic interactions: B:V.98, B:A.101, B:Y.115, B:P.118, B:I.125, C:Q.4
MYS.17: 4 residues within 4Å:- Chain C: M.256, G.257
- Ligands: LDA.1, BCL.6
No protein-ligand interaction detected (PLIP)- 4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)
BCL.5: 27 residues within 4Å:- Chain B: F.97, A.124, I.125, A.127, L.131, W.156, V.157, 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: H.197, Y.210
- Ligands: BCL.6, BPH.7, U10.9, BCL.11, BCL.12
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:F.97, B:A.124, B:V.157, B:T.160, 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.6: 20 residues within 4Å:- Chain B: Y.128, L.131, F.146, I.150, H.153, L.154, V.157
- Chain C: H.197, G.203, I.206, A.207, Y.210, G.211, L.214
- Ligands: BCL.5, BPH.7, U10.9, BCL.12, LDA.16, MYS.17
10 PLIP interactions:4 interactions with chain C, 6 interactions with chain B,- Hydrophobic interactions: C:I.206, C:I.206, C:L.214, B:Y.128, B:L.131, B:F.146, B:L.154, B:V.157
- pi-Stacking: C:Y.210
- Metal complexes: B:H.153
BCL.11: 20 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, I.179, H.182, L.183, T.186
- Ligands: BCL.5, BCL.12, BPH.13, SPN.15
10 PLIP interactions:7 interactions with chain C, 3 interactions with chain B,- Hydrophobic interactions: C:W.66, C:F.67, C:F.67, C:L.160, C:I.179, C:L.183, B:I.177, B:I.177, B:L.185
- Metal complexes: C:H.182
BCL.12: 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, H.197, H.202, S.205, I.206, L.209, Y.210, V.276, G.280, I.284
- Ligands: BCL.5, BCL.6, BCL.11, BPH.13
12 PLIP interactions:12 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:I.206, C:L.209, C:Y.210, C:V.276
- Hydrogen bonds: C:S.205
- Metal complexes: C:H.202
- 2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)
BPH.7: 25 residues within 4Å:- Chain B: 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, L.238, V.241
- Chain C: Y.210, A.213, L.214, A.217, M.218, W.252, M.256
- Ligands: BCL.5, BCL.6
14 PLIP interactions:4 interactions with chain C, 10 interactions with chain B- Hydrophobic interactions: C:Y.210, C:A.213, C:L.214, C:A.217, B:I.49, B:A.120, B:F.121, B:F.121, B:Y.148, B:L.238, B:V.241, B:V.241
- Hydrogen bonds: B:E.104
- pi-Stacking: B:F.121
BPH.13: 22 residues within 4Å:- Chain B: F.181, L.185, A.188, L.189, L.219
- Chain C: S.59, L.60, G.63, L.64, W.66, F.67, A.125, V.126, W.129, T.146, A.149, F.150, A.153, A.273, T.277
- Ligands: BCL.11, BCL.12
14 PLIP interactions:2 interactions with chain B, 12 interactions with chain C- Hydrophobic interactions: B:A.188, B:L.189, C:L.60, C:L.64, C:W.66, C:F.67, C:W.129, C:W.129, C:A.149, C:F.150, C:F.150, C:F.150, C:A.153, C:T.277
- 2 x NKP: (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate(Non-covalent)
NKP.8: 8 residues within 4Å:- Chain A: I.14, G.18, Y.21, Y.22
- Chain B: N.199
- Chain C: H.145, R.267
- Ligands: NKP.10
10 PLIP interactions:7 interactions with chain A, 2 interactions with chain C, 1 interactions with chain B- Hydrophobic interactions: A:I.14, A:Y.21, A:Y.21, A:Y.22, A:Y.22
- Water bridges: A:Y.22, A:K.54
- Salt bridges: C:H.145, C:R.267
- Hydrogen bonds: B:N.199
NKP.10: 11 residues within 4Å:- Chain C: G.143, K.144, H.145, W.148, L.151, W.155, I.270, W.271, V.274, L.278
- Ligands: NKP.8
16 PLIP interactions:16 interactions with chain C- Hydrophobic interactions: C:W.148, C:L.151, C:L.151, C:W.155, C:W.155, C:W.155, C:I.270, C:W.271, C:V.274, C:L.278
- Hydrogen bonds: C:K.144
- Water bridges: C:K.144, C:K.144, C:R.267
- Salt bridges: C:H.145, C:H.145
- 1 x U10: UBIQUINONE-10(Non-covalent)
U10.9: 24 residues within 4Å:- Chain B: V.26, F.29, G.35, F.39, W.100, R.103
- Chain C: 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: BCL.5, BCL.6
19 PLIP interactions:6 interactions with chain B, 13 interactions with chain C- Hydrophobic interactions: B:V.26, B:V.26, B:F.29, B:F.29, B:F.39, B:W.100, C:M.218, 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, C:W.268
- Hydrogen bonds: C:T.222, C:A.260
- 1 x FE: FE (III) ION(Non-covalent)
- 1 x SPN: SPEROIDENONE(Non-covalent)
SPN.15: 20 residues within 4Å:- Chain C: F.67, F.68, I.70, G.71, F.74, W.75, L.89, S.119, F.120, M.122, W.157, G.161, F.162, W.171, V.175, Y.177, G.178, I.179, H.182
- Ligands: BCL.11
12 PLIP interactions:12 interactions with chain C- Hydrophobic interactions: C:F.67, C:F.67, C:I.70, C:F.74, C:L.89, C:F.120, C:F.120, C:F.162, C:F.162, C:W.171, C:V.175, C:I.179
- 1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 1 x PO4: PHOSPHATE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Selikhanov, G. et al., X-ray structure of the Rhodobacter sphaeroides reaction center with an M197 Phe→His substitution clarifies the properties of the mutant complex. Iucrj (2022)
- Release Date
- 2022-04-27
- 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 2.04 Å
- Oligo State
- hetero-1-1-1-mer
- Ligands
- 2 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)
- 1 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)
- 3 x MYS: PENTADECANE(Non-covalent)
- 4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)
- 2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)
- 2 x NKP: (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate(Non-covalent)
- 1 x U10: UBIQUINONE-10(Non-covalent)
- 1 x FE: FE (III) ION(Non-covalent)
- 1 x SPN: SPEROIDENONE(Non-covalent)
- 1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 1 x PO4: PHOSPHATE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Selikhanov, G. et al., X-ray structure of the Rhodobacter sphaeroides reaction center with an M197 Phe→His substitution clarifies the properties of the mutant complex. Iucrj (2022)
- Release Date
- 2022-04-27
- 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.