- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.60 Å
- Oligo State
- hetero-1-1-1-mer
- Ligands
- 7 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)
- 10 x UNL: UNKNOWN LIGAND
UNL.2: 3 residues within 4Å:- Chain A: A.17
- Ligands: UNL.3, CDL.24
No protein-ligand interaction detected (PLIP)UNL.3: 3 residues within 4Å:- Chain A: Y.21, P.47
- Ligands: UNL.2
1 PLIP interactions:1 interactions with chain A- Hydrophobic interactions: A:Y.21
UNL.4: 5 residues within 4Å:- Chain A: Y.10, W.13, A.17, I.20
- Ligands: LDA.43
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:W.13, A:A.17, A:I.20
UNL.5: 2 residues within 4Å:- Chain A: W.13
- Ligands: LDA.43
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:W.13, A:W.13
UNL.15: 9 residues within 4Å:- Chain B: L.75, G.76, G.77, Q.87, T.90, I.91, T.94, L.133, W.142
2 PLIP interactions:2 interactions with chain B- Hydrophobic interactions: B:L.133, B:W.142
UNL.16: 5 residues within 4Å:- Chain B: A.101, R.109, Y.115, A.122
- Ligands: UNL.38
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:A.101, B:Y.115, B:A.122
UNL.17: 4 residues within 4Å:- Chain B: F.134, F.242, A.245, L.246
4 PLIP interactions:4 interactions with chain B- Hydrophobic interactions: B:F.134, B:F.242, B:A.245, B:L.246
UNL.36: 2 residues within 4Å:- Chain C: L.52
- Ligands: BCL.26
1 PLIP interactions:1 interactions with chain C- Hydrophobic interactions: C:L.52
UNL.37: 6 residues within 4Å:- Chain C: L.167, M.168, L.285, G.288, T.289, V.290
3 PLIP interactions:3 interactions with chain C- Hydrophobic interactions: C:L.167, C:L.285, C:V.290
UNL.38: 3 residues within 4Å:- Chain B: F.119
- Chain C: Q.4
- Ligands: UNL.16
3 PLIP interactions:1 interactions with chain C, 2 interactions with chain B- Hydrophobic interactions: C:Q.4, B:F.119, B:F.119
- 4 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.6: 2 residues within 4Å:- Chain A: H.118
- Chain C: T.21
4 PLIP interactions:3 interactions with chain C, 1 interactions with chain A- Hydrogen bonds: C:T.21, C:T.21, C:T.21
- Salt bridges: A:H.118
PO4.23: 2 residues within 4Å:- Chain B: F.123, S.239
No protein-ligand interaction detected (PLIP)PO4.39: 3 residues within 4Å:- Chain C: N.28, G.53, S.54
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:N.28, C:N.28, C:S.54, C:S.54
PO4.40: 5 residues within 4Å:- Chain C: Y.3, Q.4, N.5, I.6, F.7
6 PLIP interactions:6 interactions with chain C- Hydrogen bonds: C:Q.4, C:N.5, C:I.6, C:F.7, C:F.7, C:F.7
- 8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.7: 3 residues within 4Å:- Chain A: H.120, N.121, K.124
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:N.121, A:K.124
EDO.8: 5 residues within 4Å:- Chain A: I.57, L.58, G.61, R.62, G.63
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:G.61, A:G.63
EDO.9: 4 residues within 4Å:- Chain A: S.72, D.74, V.107, A.108
2 PLIP interactions:1 interactions with chain C, 1 interactions with chain A- Water bridges: C:D.240, A:A.108
EDO.19: 4 residues within 4Å:- Chain B: F.123, L.126, A.127, F.242
No protein-ligand interaction detected (PLIP)EDO.20: 8 residues within 4Å:- Chain A: L.233
- Chain B: C.108, G.112, I.113, G.114, Y.115
- Chain C: E.2, R.228
3 PLIP interactions:1 interactions with chain B, 2 interactions with chain C- Hydrogen bonds: B:C.108, C:R.228, C:R.228
EDO.21: 5 residues within 4Å:- Chain B: Y.162, G.165, N.166
- Chain C: N.187, L.191
2 PLIP interactions:1 interactions with chain C, 1 interactions with chain B- Hydrogen bonds: C:N.187, B:G.165
EDO.41: 9 residues within 4Å:- Chain A: R.169, F.170, Q.186, C.226
- Chain C: S.227, R.228, F.229, G.230, R.233
5 PLIP interactions:3 interactions with chain C, 2 interactions with chain A- Hydrogen bonds: C:R.228, C:G.230, C:R.233, A:R.169, A:Q.186
EDO.42: 8 residues within 4Å:- Chain A: Q.186
- Chain B: H.116
- Chain C: Y.3, Q.4, L.224, A.225, S.227, R.228
5 PLIP interactions:5 interactions with chain C- Hydrogen bonds: C:Y.3, C:L.224, C:S.227, C:R.228, C:R.228
- 1 x K: POTASSIUM ION(Non-covalent)
- 4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)
BCL.11: 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, 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.12, BPH.13, BCL.25, BCL.26, U10.29, LDA.43
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: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.12: 22 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: F.197, G.203, I.206, A.207, Y.210, G.211, L.214
- Ligands: BCL.11, BPH.13, HTO.22, BCL.26, U10.29, LDA.31
14 PLIP interactions:8 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: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
BCL.25: 17 residues within 4Å:- Chain B: H.168, M.174, I.177, T.178, F.181, T.182
- Chain C: F.67, M.122, W.157, I.179, H.182, L.183, T.186
- Ligands: BCL.11, BCL.26, BPH.27, SPN.30
8 PLIP interactions:5 interactions with chain B, 3 interactions with chain C,- Hydrophobic interactions: B:I.177, B:I.177, B:T.182, C:F.67, C:L.183
- Hydrogen bonds: B:T.178, B:T.182
- Metal complexes: C:H.182
BCL.26: 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, Y.210, V.276, G.280, I.284
- Ligands: BCL.11, BCL.12, BCL.25, BPH.27, UNL.36
11 PLIP interactions:11 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:Y.210, C:V.276
- Hydrogen bonds: C:S.205
- Metal complexes: C:H.202
- 2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)
BPH.13: 30 residues within 4Å:- Chain B: T.38, F.41, A.42, G.45, 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, M.218, W.252, M.256
- Ligands: BCL.11, BCL.12
19 PLIP interactions:16 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.123, B:A.124, B:Y.128, B:Y.148, B:I.150, B:L.238, B:V.241, B:V.241, C:Y.210, C:A.213, C:L.214
- pi-Stacking: B:F.121
BPH.27: 25 residues within 4Å:- Chain B: F.181, A.184, 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, T.277
- Ligands: BCL.25, BCL.26
12 PLIP interactions:10 interactions with chain C, 2 interactions with chain B- Hydrophobic interactions: C:L.64, C:W.66, C:W.129, 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:L.189
- 2 x U10: UBIQUINONE-10(Non-covalent)
U10.14: 16 residues within 4Å:- Chain B: T.178, T.182, L.189, H.190, L.193, V.194, E.212, D.213, F.216, Y.222, S.223, I.224, G.225, T.226, I.229
- Ligands: DIO.18
11 PLIP interactions:11 interactions with chain B- Hydrophobic interactions: B:T.178, B:T.182, B:L.189, B:L.193, B:Y.222, B:I.224, B:I.229, B:I.229
- Hydrogen bonds: B:H.190, B:I.224, B:G.225
U10.29: 23 residues within 4Å:- Chain B: G.35, F.39, W.100, R.103
- Chain C: L.214, M.218, H.219, T.222, 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.11, BCL.12, LDA.43
14 PLIP interactions:11 interactions with chain C, 3 interactions with chain B- Hydrophobic interactions: C:L.214, C:M.218, C:W.252, C:M.256, C:F.258, C:F.258, C:A.260, C:W.268, C:W.268, B:F.39, B:W.100, B:W.100
- Hydrogen bonds: C:T.222, C:A.260
- 1 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)
- 1 x HTO: HEPTANE-1,2,3-TRIOL(Non-covalent)
- 1 x CDL: CARDIOLIPIN(Non-covalent)
CDL.24: 20 residues within 4Å:- Chain A: A.8, I.14, F.15, G.18, L.19, Y.22
- Chain B: N.199, P.200
- Chain C: G.143, K.144, H.145, W.148, W.155, R.267, I.270, W.271, V.274, L.278, I.282
- Ligands: UNL.2
23 PLIP interactions:18 interactions with chain C, 4 interactions with chain A, 1 interactions with chain B- Hydrophobic interactions: C:W.148, C:W.148, C:W.155, C:W.155, C:I.270, C:V.274, C:L.278, C:L.278, C:I.282, A:I.14, A:L.19, A:Y.22, A:Y.22
- Hydrogen bonds: C:K.144, B:N.199
- Water bridges: C:K.144, C:R.267, C:R.267, C:R.267
- Salt bridges: C:H.145, C:H.145, C:H.145, C:R.267
- 1 x FE: FE (III) ION(Non-covalent)
- 1 x SPN: SPEROIDENONE(Non-covalent)
SPN.30: 22 residues within 4Å:- Chain C: F.67, F.68, I.70, G.71, I.72, F.74, W.75, W.115, S.119, F.120, M.122, F.123, W.157, L.160, G.161, F.162, W.171, V.175, Y.177, I.179, H.182
- Ligands: BCL.25
20 PLIP interactions:20 interactions with chain C- Hydrophobic interactions: C:F.67, C:F.67, C:F.67, C:I.70, C:I.70, C:I.72, C:F.74, C:W.115, C:F.120, C:F.123, C:W.157, C:L.160, C:F.162, C:W.171, C:V.175, C:V.175, C:Y.177, C:Y.177, C:I.179, C:H.182
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Selikhanov, G. et al., Stabilization of Cereibacter sphaeroides Photosynthetic Reaction Center by the Introduction of Disulfide Bonds. Membranes (Basel) (2023)
- Release Date
- 2023-11-22
- 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 2.60 Å
- Oligo State
- hetero-1-1-1-mer
- Ligands
- 7 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)
- 10 x UNL: UNKNOWN LIGAND
- 4 x PO4: PHOSPHATE ION(Non-functional Binders)
- 8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 1 x K: POTASSIUM ION(Non-covalent)
- 4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)
- 2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)
- 2 x U10: UBIQUINONE-10(Non-covalent)
- 1 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)
- 1 x HTO: HEPTANE-1,2,3-TRIOL(Non-covalent)
- 1 x CDL: CARDIOLIPIN(Non-covalent)
- 1 x FE: FE (III) ION(Non-covalent)
- 1 x SPN: SPEROIDENONE(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Selikhanov, G. et al., Stabilization of Cereibacter sphaeroides Photosynthetic Reaction Center by the Introduction of Disulfide Bonds. Membranes (Basel) (2023)
- Release Date
- 2023-11-22
- 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.