- 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)
- 6 x D12: DODECANE(Non-covalent)
D12.3: 6 residues within 4Å:- Chain A: A.16, I.19, Y.20
- Ligands: D12.4, D12.5, CDL.44
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:I.19, A:Y.20
D12.4: 4 residues within 4Å:- Chain A: Y.20, P.46, F.47
- Ligands: D12.3
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:Y.20, A:Y.20, A:P.46
D12.5: 7 residues within 4Å:- Chain A: W.12, L.15, I.19
- Ligands: LDA.1, D12.3, MYS.6, LDA.50
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:W.12, A:W.12, A:L.15, A:I.19
D12.19: 8 residues within 4Å:- Chain B: L.75, G.76, G.77, Q.87, T.90, I.91, L.133, W.142
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:Q.87, B:L.133, B:W.142
D12.42: 4 residues within 4Å:- Chain A: L.3
- Chain C: L.167, G.288, T.289
2 PLIP interactions:1 interactions with chain C, 1 interactions with chain A- Hydrophobic interactions: C:L.167, A:L.3
D12.43: 7 residues within 4Å:- Chain B: Y.115, H.116, F.119
- Chain C: E.2, Q.4, I.6
- Ligands: MYS.20
6 PLIP interactions:2 interactions with chain C, 4 interactions with chain B- Hydrophobic interactions: C:E.2, C:I.6, B:Y.115, B:F.119, B:F.119, B:F.119
- 3 x MYS: PENTADECANE(Non-covalent)
MYS.6: 5 residues within 4Å:- Chain A: Y.9, W.12
- Ligands: D12.5, HTO.29, LDA.50
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:Y.9, A:W.12, A:W.12, A:W.12
MYS.20: 6 residues within 4Å:- Chain B: A.101, R.109, Y.115, P.118, A.122
- Ligands: D12.43
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:A.101, B:Y.115, B:A.122
MYS.41: 6 residues within 4Å:- Chain B: V.220
- Chain C: I.50, L.52, W.129
- Ligands: LDA.18, BCL.32
3 PLIP interactions:3 interactions with chain C- Hydrophobic interactions: C:I.50, C:L.52, C:W.129
- 3 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.7: 2 residues within 4Å:- Chain A: H.117
- Chain C: T.21
2 PLIP interactions:1 interactions with chain A, 1 interactions with chain C- Salt bridges: A:H.117
- Hydrogen bonds: C:T.21
PO4.45: 3 residues within 4Å:- Chain C: N.28, G.53, S.54
6 PLIP interactions:6 interactions with chain C- Hydrogen bonds: C:N.28, C:N.28, C:S.54, C:S.54
- Water bridges: C:Y.51, C:L.55
PO4.46: 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
- 13 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.8: 2 residues within 4Å:- Chain A: N.43
- Chain B: A.1
4 PLIP interactions:2 interactions with chain A, 2 interactions with chain B- Hydrogen bonds: A:N.43, B:A.1
- Water bridges: A:E.85, B:A.1
EDO.9: 3 residues within 4Å:- Chain A: H.119, N.120, K.123
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:N.120, A:N.120, A:K.123
EDO.10: 3 residues within 4Å:- Chain A: Q.190, S.191, N.192
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:S.191
EDO.11: 5 residues within 4Å:- Chain A: I.56, L.57, G.60, R.61, G.62
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:G.60, A:G.60, A:G.62
EDO.12: 5 residues within 4Å:- Chain A: S.71, E.72, V.106, A.107
- Chain C: R.241
5 PLIP interactions:2 interactions with chain C, 3 interactions with chain A- Hydrogen bonds: C:R.241, A:A.107
- Water bridges: C:R.241, A:S.71, A:S.71
EDO.23: 3 residues within 4Å:- Chain B: F.123, S.239, F.242
No protein-ligand interaction detected (PLIP)EDO.24: 5 residues within 4Å:- Chain B: F.123, L.126, V.241, F.242, A.245
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:V.241
EDO.25: 8 residues within 4Å:- Chain A: L.232
- Chain B: C.108, G.112, I.113, G.114, Y.115
- Chain C: E.2, R.228
7 PLIP interactions:2 interactions with chain B, 5 interactions with chain C- Water bridges: B:R.109, B:G.112, C:E.2, C:Q.4, C:Q.4
- Hydrogen bonds: C:R.228, C:R.228
EDO.26: 5 residues within 4Å:- Chain B: Y.162, G.165, N.166
- Chain C: N.187, L.191
4 PLIP interactions:1 interactions with chain C, 3 interactions with chain B- Hydrogen bonds: C:N.187, B:N.166
- Water bridges: B:Y.162, B:Q.258
EDO.27: 3 residues within 4Å:- Chain B: W.151
- Chain C: Y.198, G.298
No protein-ligand interaction detected (PLIP)EDO.47: 9 residues within 4Å:- Chain A: R.168, F.169, Q.185, C.225
- Chain C: S.227, R.228, F.229, G.230, R.233
4 PLIP interactions:2 interactions with chain C, 2 interactions with chain A- Hydrogen bonds: C:G.230, C:R.233, A:R.168, A:Q.185
EDO.48: 8 residues within 4Å:- Chain A: Q.185
- 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:S.227, C:S.227, C:R.228, C:R.228
EDO.49: 4 residues within 4Å:- Chain C: W.127, L.151, I.154, W.155
No protein-ligand interaction detected (PLIP)- 1 x NA: SODIUM ION(Non-functional Binders)
- 1 x K: POTASSIUM ION(Non-covalent)
- 4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)
BCL.15: 30 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: BPH.16, BCL.31, BCL.32, BCL.33, U10.36, LDA.50
16 PLIP interactions:15 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:I.177, B:F.180, B:F.180, C:Y.210
- Hydrogen bonds: B:S.244
- Metal complexes: B:H.173
BCL.31: 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, T.186
- Ligands: BCL.15, U10.17, BCL.32, BPH.34, SPN.37
11 PLIP interactions:5 interactions with chain B, 6 interactions with chain C,- Hydrophobic interactions: B:I.177, B:I.177, B:L.185, C:W.66, C:F.67, C:L.160, C:V.175, C:L.183
- Hydrogen bonds: B:T.178, B:T.182
- Metal complexes: C:H.182
BCL.32: 29 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, F.197, H.202, S.205, I.206, L.209, Y.210, V.276, G.280, I.284
- Ligands: BCL.15, BCL.31, BCL.33, BPH.34, MYS.41
14 PLIP interactions:14 interactions with chain C,- Hydrophobic interactions: C:V.126, C:V.126, 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, C:I.284
- Metal complexes: C:H.202
BCL.33: 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: LDA.1, BCL.15, BPH.16, BCL.32, U10.36, LDA.50
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
- 2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)
BPH.16: 32 residues within 4Å:- Chain B: T.38, 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, A.217, M.218, W.252, T.255, M.256
- Ligands: BCL.15, BCL.33, U10.36
20 PLIP interactions:4 interactions with chain C, 16 interactions with chain B- Hydrophobic interactions: C:Y.210, C:A.213, C:L.214, C:A.217, B:A.42, B:I.49, B:A.93, 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:Y.148, B:L.238, B:V.241, B:V.241
BPH.34: 26 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, 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: BCL.31, BCL.32, SPN.37
18 PLIP interactions:15 interactions with chain C, 3 interactions with chain B- Hydrophobic interactions: C:L.64, C:W.66, C:F.67, C:F.67, C:F.67, C:A.125, 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:A.188, B:L.189
- pi-Stacking: C:F.150
- 2 x U10: UBIQUINONE-10(Non-covalent)
U10.17: 20 residues within 4Å:- Chain B: P.171, T.178, F.179, 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, L.232, W.263
- Ligands: BCL.31
17 PLIP interactions:17 interactions with chain B- Hydrophobic interactions: B:P.171, B:F.179, B:F.179, B:T.182, B:L.189, B:L.193, B:F.216, B:Y.222, B:I.224, B:I.229, B:I.229, B:L.232, B:L.232, B:W.263
- Hydrogen bonds: B:H.190, B:I.224, B:G.225
U10.36: 25 residues within 4Å:- Chain B: F.29, Y.30, G.35, 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: BCL.15, BPH.16, BCL.33, LDA.50
19 PLIP interactions:13 interactions with chain C, 6 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:I.265, C:I.265, C:W.268, C:W.268, B:F.29, B:F.29, B:F.29, B:W.100, B:W.100, B:W.100
- Hydrogen bonds: C:T.222, C:A.260
- 1 x D10: DECANE(Non-covalent)
- 1 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)
- 3 x HTO: HEPTANE-1,2,3-TRIOL(Non-covalent)
HTO.28: 2 residues within 4Å:- Chain B: M.139, T.253
2 PLIP interactions:2 interactions with chain B- Water bridges: B:M.139, B:Y.144
HTO.29: 7 residues within 4Å:- Chain B: I.49, P.61, I.64, Y.148, G.149, I.150
- Ligands: MYS.6
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:P.61
- Hydrogen bonds: B:Y.148, B:I.150
HTO.30: 2 residues within 4Å:- Chain B: N.60, L.63
No protein-ligand interaction detected (PLIP)- 1 x FE: FE (III) ION(Non-covalent)
- 1 x SPN: SPEROIDENONE(Non-covalent)
SPN.37: 23 residues within 4Å:- Chain C: F.67, F.68, I.70, G.71, F.74, W.75, F.85, 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.31, BPH.34
17 PLIP interactions:17 interactions with chain C- Hydrophobic interactions: C:F.67, C:F.67, C:F.67, C:I.70, C:F.74, C:F.74, C:F.85, C:W.115, C:F.120, C:W.157, C:L.160, C:F.162, C:W.171, C:V.175, C:Y.177, C:Y.177, C:I.179
- 1 x CDL: CARDIOLIPIN(Non-covalent)
CDL.44: 21 residues within 4Å:- Chain A: A.7, I.13, F.14, G.17, L.18, Y.21
- Chain B: N.199, P.200
- Chain C: G.143, K.144, H.145, W.148, L.151, W.155, R.267, I.270, W.271, V.274, L.278, I.282
- Ligands: D12.3
30 PLIP interactions:20 interactions with chain C, 8 interactions with chain A, 2 interactions with chain B- Hydrophobic interactions: C:W.148, C:W.148, C:W.148, C:W.155, C:W.155, C:I.270, C:W.271, C:V.274, C:L.278, C:L.278, C:I.282, A:F.14, A:F.14, A:F.14, A:F.14, A:L.18, A:Y.21
- Hydrogen bonds: C:K.144, B:N.199
- Water bridges: C:K.144, C:K.144, C:K.144, C:R.267, A:Y.21, A:K.53, B:N.199
- Salt bridges: C:H.145, C:H.145, 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
- 7 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)
- 6 x D12: DODECANE(Non-covalent)
- 3 x MYS: PENTADECANE(Non-covalent)
- 3 x PO4: PHOSPHATE ION(Non-functional Binders)
- 13 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 1 x NA: SODIUM ION(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 D10: DECANE(Non-covalent)
- 1 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)
- 3 x HTO: HEPTANE-1,2,3-TRIOL(Non-covalent)
- 1 x FE: FE (III) ION(Non-covalent)
- 1 x SPN: SPEROIDENONE(Non-covalent)
- 1 x CDL: CARDIOLIPIN(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.