- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.22 Å
- Oligo State
- hetero-1-1-1-mer
- Ligands
- 4 x MYS: PENTADECANE(Non-covalent)
- 2 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)
LDA.2: 10 residues within 4Å:- Chain A: Q.24, Y.32, L.34, F.48
- Chain C: R.253, G.257, F.258
- Ligands: MYS.3, U10.12, LDA.18
5 PLIP interactions:1 interactions with chain A, 4 interactions with chain C- Hydrophobic interactions: A:F.48, C:F.258, C:F.258
- Hydrogen bonds: C:R.253, C:R.253
LDA.18: 7 residues within 4Å:- Chain A: W.13
- Chain C: P.200, A.207, F.208, W.268
- Ligands: LDA.2, BCL.8
4 PLIP interactions:3 interactions with chain C, 1 interactions with chain A- Hydrophobic interactions: C:A.207, C:F.208, C:W.268, A:W.13
- 1 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)
OLC.4: 14 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
9 PLIP interactions:9 interactions with chain B- Hydrophobic interactions: B:L.189, B:L.189, B:F.216, B:Y.222, B:I.229
- Hydrogen bonds: B:S.223, B:I.224, B:G.225
- Salt bridges: B:H.190
- 4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)
BCL.7: 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.8, BPH.10, U10.12, BCL.15, BCL.16
12 PLIP interactions:11 interactions with chain B, 1 interactions with chain C,- Hydrophobic interactions: B:F.97, B:F.97, B:A.124, B:T.160, B:Y.162, 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: 21 residues within 4Å:- Chain B: I.46, I.49, 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.7, BPH.10, U10.12, BCL.16, LDA.18
12 PLIP interactions:8 interactions with chain B, 4 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:V.157, C:I.206, C:I.206, C:L.214
- Metal complexes: B:H.153
- pi-Stacking: C:Y.210
BCL.15: 18 residues within 4Å:- Chain B: H.168, M.174, I.177, T.178, F.181, T.182
- Chain C: W.66, M.122, W.157, I.179, H.182, L.183, W.185, T.186
- Ligands: BCL.7, BPH.9, SPN.14, BCL.16
9 PLIP interactions:6 interactions with chain C, 3 interactions with chain B,- Hydrophobic interactions: C:W.66, C:I.179, C:L.183, C:W.185, C:T.186, B:I.177, B:I.177, B:T.182
- Metal complexes: C:H.182
BCL.16: 28 residues within 4Å:- Chain B: V.157, Y.162, H.168, F.181
- Chain C: M.122, V.126, 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.7, BCL.8, BPH.9, BCL.15
13 PLIP interactions:13 interactions with chain C,- Hydrophobic interactions: C:V.126, C:A.153, C:L.156, C:W.157, C:T.186, C:N.187, C:F.189, C:L.196, C:I.206, C:L.209, C:Y.210, C:V.276
- Metal complexes: C:H.202
- 2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)
BPH.9: 22 residues within 4Å:- Chain B: F.181, A.184, L.185, A.188, L.189, L.219
- Chain C: S.59, L.60, G.63, L.64, F.67, A.125, V.126, W.129, T.146, A.149, F.150, A.153, A.273, T.277
- Ligands: BCL.15, BCL.16
14 PLIP interactions:12 interactions with chain C, 2 interactions with chain B- Hydrophobic interactions: C:L.60, C:F.67, C:F.67, C:A.125, C:W.129, C:A.149, C:F.150, C:F.150, C:F.150, C:A.153, C:T.277, B:A.184, B:A.188
- pi-Stacking: C:F.150
BPH.10: 26 residues within 4Å:- Chain B: F.41, 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, M.218, W.252, T.255, M.256
- Ligands: BCL.7, BCL.8
15 PLIP interactions:3 interactions with chain C, 12 interactions with chain B- Hydrophobic interactions: C:Y.210, C:A.213, C:L.214, B:I.49, B:A.93, B:A.120, B:F.121, B:F.121, B:F.121, B:A.124, B:Y.148, B:L.238, B:V.241, B:V.241
- Hydrogen bonds: B:E.104
- 2 x NKP: (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate(Non-covalent)
NKP.11: 10 residues within 4Å:- Chain A: I.14, F.15, G.18, L.19, Y.21, Y.22
- Chain B: N.199
- Chain C: H.145, R.267
- Ligands: NKP.13
7 PLIP interactions:4 interactions with chain A, 1 interactions with chain B, 2 interactions with chain C- Hydrophobic interactions: A:L.19, A:Y.21, A:Y.22
- Hydrogen bonds: A:Y.22, B:N.199
- Salt bridges: C:H.145, C:R.267
NKP.13: 11 residues within 4Å:- Chain C: G.143, K.144, H.145, W.148, W.155, I.270, W.271, V.274, L.278
- Ligands: MYS.1, NKP.11
14 PLIP interactions:14 interactions with chain C- Hydrophobic interactions: C:W.148, C:W.155, 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
- Salt bridges: C:H.145, C:H.145
- 1 x U10: UBIQUINONE-10(Non-covalent)
U10.12: 26 residues within 4Å:- Chain A: S.85, F.88
- Chain B: V.26, F.29, G.35, T.38, 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
- Ligands: LDA.2, BCL.7, BCL.8
20 PLIP interactions:13 interactions with chain C, 6 interactions with chain B, 1 interactions with chain A- Hydrophobic interactions: 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, B:V.26, B:F.29, B:F.29, B:T.38, B:W.100, B:W.100, A:F.88
- Hydrogen bonds: C:T.222, C:A.260
- 1 x SPN: SPEROIDENONE(Non-covalent)
SPN.14: 21 residues within 4Å:- Chain C: F.67, F.68, I.70, G.71, F.74, W.75, W.115, S.119, F.120, M.122, W.157, G.161, F.162, W.171, V.175, P.176, Y.177, G.178, I.179, H.182
- Ligands: BCL.15
14 PLIP interactions:14 interactions with chain C- Hydrophobic interactions: C:F.67, C:F.67, C:F.67, C:I.70, C:W.115, C:W.157, C:F.162, C:F.162, C:W.171, C:V.175, C:V.175, C:Y.177, C:I.179
- Hydrogen bonds: C:G.71
- 1 x FE: FE (III) ION(Non-covalent)
- 1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Gabdulkhakov, A.G. et al., X-Ray structure of Rhodobacter sphaeroides reaction center with M197 Phe-His substitution clarifies properties of the mutant complex. To Be Published
- Release Date
- 2022-07-13
- 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
HB
LC
M - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.22 Å
- Oligo State
- hetero-1-1-1-mer
- Ligands
- 4 x MYS: PENTADECANE(Non-covalent)
- 2 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)
- 1 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(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 SPN: SPEROIDENONE(Non-covalent)
- 1 x FE: FE (III) ION(Non-covalent)
- 1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Gabdulkhakov, A.G. et al., X-Ray structure of Rhodobacter sphaeroides reaction center with M197 Phe-His substitution clarifies properties of the mutant complex. To Be Published
- Release Date
- 2022-07-13
- 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
HB
LC
M - Membrane
-
We predict this structure to be a membrane protein.