- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.80 Å
- Oligo State
- hetero-1-1-1-mer
- Ligands
- 8 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)
- 4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)
BCL.4: 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: LDA.3, BPH.5, BCL.9, BCL.10, BCL.11, U10.14
15 PLIP interactions:14 interactions with chain B, 1 interactions with chain C,- Hydrophobic interactions: B:F.97, B:F.97, B:A.124, B:Y.128, B:V.157, 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.9: 19 residues within 4Å:- Chain B: H.168, M.174, I.177, T.178, F.181, T.182
- Chain C: F.67, L.89, M.122, W.157, L.160, I.179, H.182, L.183, T.186
- Ligands: BCL.4, BCL.10, BPH.12, SPN.15
10 PLIP interactions:3 interactions with chain B, 7 interactions with chain C,- Hydrophobic interactions: B:I.177, B:I.177, C:F.67, C:L.89, C:L.160, C:I.179, C:L.183, C:T.186
- pi-Stacking: B:F.181
- Metal complexes: C:H.182
BCL.10: 27 residues within 4Å:- Chain B: V.157, Y.162, H.168, F.181
- Chain C: W.66, M.122, 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.4, BCL.9, BCL.11, BPH.12
12 PLIP interactions:12 interactions with chain C,- Hydrophobic interactions: C:W.66, C:L.156, C:W.157, C:W.157, C:T.186, C:N.187, C:F.189, C:L.196, C:I.206, C:Y.210, C:V.276
- Metal complexes: C:H.202
BCL.11: 19 residues within 4Å:- Chain B: I.46, Y.128, F.146, I.150, W.151, H.153, L.154
- Chain C: F.197, G.203, I.206, A.207, Y.210, G.211, L.214
- Ligands: BCL.4, BPH.5, BCL.10, U10.14, LDA.16
11 PLIP interactions:6 interactions with chain C, 5 interactions with chain B,- Hydrophobic interactions: C:F.197, C:I.206, C:I.206, C:Y.210, C:L.214, B:I.46, B:Y.128, B:F.146, B:L.154
- pi-Stacking: C:Y.210
- Metal complexes: B:H.153
- 2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)
BPH.5: 29 residues within 4Å:- Chain B: T.38, A.42, 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, H.153, L.238, V.241
- Chain C: Y.210, A.213, L.214, A.217, M.218, W.252, M.256
- Ligands: BCL.4, BCL.11, U10.14
17 PLIP interactions:2 interactions with chain C, 15 interactions with chain B- Hydrophobic interactions: C:Y.210, C:A.213, B:A.42, B:I.49, B:A.96, B:F.97, B:A.120, B:F.121, B:F.121, B:F.123, B:Y.128, B:Y.148, B:L.238, B:V.241, B:V.241
- Hydrogen bonds: B:E.104
- pi-Stacking: B:F.121
BPH.12: 22 residues within 4Å:- Chain B: F.181, L.185, L.189, L.219, V.220
- Chain C: S.59, L.60, G.63, L.64, F.67, A.125, V.126, W.129, T.133, T.146, A.149, F.150, A.153, A.273, T.277
- Ligands: BCL.9, BCL.10
10 PLIP interactions:7 interactions with chain C, 3 interactions with chain B- Hydrophobic interactions: C:L.64, C:F.67, C:F.67, C:A.149, C:F.150, C:F.150, B:F.181, B:L.185, B:L.189
- pi-Stacking: C:F.150
- 2 x U10: UBIQUINONE-10(Non-covalent)
U10.6: 16 residues within 4Å:- Chain B: I.175, T.178, F.179, T.182, L.189, H.190, L.193, F.216, Y.222, S.223, I.224, G.225, T.226, I.229, L.232, F.243
12 PLIP interactions:12 interactions with chain B- Hydrophobic interactions: B:I.175, B:T.178, B:F.179, B:T.182, B:F.216, B:F.216, B:I.224, B:L.232, B:F.243
- Hydrogen bonds: B:I.224, B:G.225
- pi-Stacking: B:F.216
U10.14: 24 residues within 4Å:- Chain B: F.29, G.35, T.38, 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, I.265, W.268
- Ligands: LDA.1, BCL.4, BPH.5, BCL.11, LDA.19
15 PLIP interactions:4 interactions with chain B, 11 interactions with chain C- Hydrophobic interactions: B:F.29, B:T.38, B:W.100, B:W.100, C:L.214, C:M.218, C:W.252, C:M.256, C:F.258, C:A.260, C:I.265, C:I.265, C:W.268, C:W.268
- Hydrogen bonds: C:A.260
- 3 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)
DIO.7: 3 residues within 4Å:- Chain B: W.263, W.266
- Chain C: F.90
1 PLIP interactions:1 interactions with chain C- Water bridges: C:F.90
DIO.8: 3 residues within 4Å:- Chain B: F.123, S.239, F.242
No protein-ligand interaction detected (PLIP)DIO.24: 2 residues within 4Å:- Chain B: F.119
- Chain C: Q.4
No protein-ligand interaction detected (PLIP)- 1 x FE: FE (III) ION(Non-covalent)
- 1 x SPN: SPEROIDENONE(Non-covalent)
SPN.15: 19 residues within 4Å:- Chain C: F.67, F.68, I.70, G.71, W.75, F.85, F.105, S.119, M.122, W.157, L.160, G.161, F.162, W.171, V.175, G.178, I.179, H.182
- Ligands: BCL.9
13 PLIP interactions:13 interactions with chain C- Hydrophobic interactions: C:F.67, C:F.67, C:F.67, C:I.70, C:F.105, C:F.105, C:W.157, C:L.160, C:F.162, C:W.171, C:V.175, C:I.179, C:H.182
- 3 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.21: 6 residues within 4Å:- Chain B: N.199
- Chain C: H.145, R.267
- Ligands: LDA.2, LDA.17, PO4.22
3 PLIP interactions:2 interactions with chain C, 1 interactions with chain B- Salt bridges: C:H.145, C:R.267
- Hydrogen bonds: B:N.199
PO4.22: 5 residues within 4Å:- Chain C: G.143, K.144, H.145
- Ligands: LDA.17, PO4.21
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:K.144
- Salt bridges: C:K.144
PO4.23: 3 residues within 4Å:- Chain C: N.28, G.53, S.54
5 PLIP interactions:5 interactions with chain C- Hydrogen bonds: C:N.28, C:S.54, C:S.54, C:S.54
- Water bridges: C:S.54
- 1 x CL: CHLORIDE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Vasilieva, L.G. et al., The site-directed mutation I(L177)H in Rhodobacter sphaeroides reaction center affects coordination of P(A) and B(B) bacteriochlorophylls. Biochim.Biophys.Acta (2012)
- Release Date
- 2012-03-14
- 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 2.80 Å
- Oligo State
- hetero-1-1-1-mer
- Ligands
- 8 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)
- 4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)
- 2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)
- 2 x U10: UBIQUINONE-10(Non-covalent)
- 3 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)
- 1 x FE: FE (III) ION(Non-covalent)
- 1 x SPN: SPEROIDENONE(Non-covalent)
- 3 x PO4: PHOSPHATE ION(Non-functional Binders)
- 1 x CL: CHLORIDE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Vasilieva, L.G. et al., The site-directed mutation I(L177)H in Rhodobacter sphaeroides reaction center affects coordination of P(A) and B(B) bacteriochlorophylls. Biochim.Biophys.Acta (2012)
- Release Date
- 2012-03-14
- 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.