- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.20 Å
- Oligo State
- hetero-1-1-1-mer
- Ligands
- 6 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)
- 2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)
BPH.3: 31 residues within 4Å:- Chain A: T.39, I.50, C.93, A.94, A.97, F.98, W.101, E.105, I.118, A.121, F.122, F.124, A.125, Y.129, Y.149, G.150, I.151, H.154, L.239, V.242
- Chain B: Y.211, A.214, G.215, A.218, M.219, W.253, T.256, M.257
- Ligands: BCL.5, BCL.15, U10.20
16 PLIP interactions:13 interactions with chain A, 3 interactions with chain B- Hydrophobic interactions: A:I.50, A:A.97, A:A.121, A:F.122, A:F.122, A:F.122, A:F.124, A:Y.129, A:Y.149, A:Y.149, A:L.239, A:V.242, A:V.242, B:Y.211, B:A.214, B:A.218
BPH.13: 21 residues within 4Å:- Chain A: F.182, A.185, L.186, L.190, L.220
- Chain B: S.60, G.64, F.68, A.126, V.127, W.130, T.134, T.147, A.150, F.151, A.154, A.274, V.275, T.278
- Ligands: BCL.16, BCL.17
13 PLIP interactions:9 interactions with chain B, 4 interactions with chain A- Hydrophobic interactions: B:F.68, B:W.130, B:W.130, B:A.150, B:F.151, B:F.151, B:A.154, B:T.278, A:F.182, A:A.185, A:L.186, A:L.190
- pi-Stacking: B:F.151
- 2 x U10: UBIQUINONE-10(Non-covalent)
U10.4: 14 residues within 4Å:- Chain A: T.183, L.190, H.191, L.194, V.195, E.213, D.214, F.217, S.224, I.225, G.226, T.227, I.230
- Ligands: LDA.2
11 PLIP interactions:11 interactions with chain A- Hydrophobic interactions: A:T.183, A:L.190, A:L.194, A:F.217, A:I.225, A:I.225, A:I.230, A:I.230
- Hydrogen bonds: A:H.191, A:I.225, A:G.226
U10.20: 26 residues within 4Å:- Chain A: F.30, Y.31, G.36, T.39, W.101, R.104
- Chain B: M.219, H.220, T.223, I.224, A.249, A.250, W.253, M.257, F.259, N.260, A.261, T.262, M.263, I.266, W.269, M.273
- Ligands: BPH.3, BCL.5, BCL.15, LDA.30
15 PLIP interactions:11 interactions with chain B, 4 interactions with chain A- Hydrophobic interactions: B:M.219, B:W.253, B:M.257, B:F.259, B:A.261, B:I.266, B:I.266, B:W.269, B:W.269, A:F.30, A:T.39, A:W.101, A:W.101
- Hydrogen bonds: B:T.223, B:A.261
- 4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)
BCL.5: 29 residues within 4Å:- Chain A: F.98, A.125, I.126, A.128, Y.129, L.132, W.157, V.158, S.159, T.161, G.162, Y.163, N.167, F.168, H.169, H.174, A.177, I.178, F.181, S.245, A.246, C.248, M.249
- Chain B: Y.211
- Ligands: BPH.3, BCL.15, BCL.16, BCL.17, U10.20
19 PLIP interactions:18 interactions with chain A, 1 interactions with chain B,- Hydrophobic interactions: A:F.98, A:F.98, A:F.98, A:F.98, A:A.125, A:A.128, A:V.158, A:T.161, A:Y.163, A:F.168, A:A.177, A:I.178, A:I.178, A:F.181, A:F.181, B:Y.211
- Hydrogen bonds: A:S.245
- pi-Cation interactions: A:H.174
- Metal complexes: A:H.174
BCL.15: 19 residues within 4Å:- Chain A: I.47, I.50, Y.129, L.132, F.147, I.151, H.154, L.155, V.158
- Chain B: F.198, G.204, I.207, A.208, Y.211, G.212
- Ligands: BPH.3, BCL.5, BCL.17, U10.20
12 PLIP interactions:7 interactions with chain A, 5 interactions with chain B,- Hydrophobic interactions: A:I.47, A:I.50, A:L.132, A:F.147, A:L.155, A:V.158, B:F.198, B:I.207, B:I.207, B:Y.211
- Metal complexes: A:H.154
- pi-Stacking: B:Y.211
BCL.16: 20 residues within 4Å:- Chain A: H.169, M.175, I.178, S.179, F.182, T.183
- Chain B: W.67, F.68, M.123, W.158, L.161, I.180, H.183, L.184, T.187
- Ligands: LDA.1, BCL.5, BPH.13, BCL.17, SPO.21
10 PLIP interactions:6 interactions with chain B, 4 interactions with chain A,- Hydrophobic interactions: B:W.67, B:F.68, B:L.161, B:I.180, B:L.184, A:I.178, A:I.178
- Metal complexes: B:H.183
- Hydrogen bonds: A:T.183
- pi-Stacking: A:F.182
BCL.17: 30 residues within 4Å:- Chain A: V.158, Y.163, H.169, F.182
- Chain B: M.123, V.127, A.154, L.157, W.158, L.161, T.187, N.188, F.190, S.191, N.196, L.197, F.198, H.203, S.206, I.207, L.210, Y.211, V.277, G.281, I.285
- Ligands: BCL.5, BPH.13, BCL.15, BCL.16, PC1.22
15 PLIP interactions:14 interactions with chain B, 1 interactions with chain A,- Hydrophobic interactions: B:V.127, B:A.154, B:L.157, B:W.158, B:T.187, B:F.190, B:L.197, B:F.198, B:I.207, B:L.210, B:Y.211, B:V.277, B:I.285, A:V.158
- Metal complexes: B:H.203
- 3 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.6: 3 residues within 4Å:- Chain A: E.73, Y.74, K.83
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:Y.74, A:Y.74, A:Y.74
- Salt bridges: A:K.83
PO4.23: 3 residues within 4Å:- Chain B: N.29, G.54, S.55
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:N.29, B:N.29, B:S.55
PO4.25: 6 residues within 4Å:- Chain A: N.200
- Chain B: H.146, R.268
- Ligands: LDA.26, GOL.27, LDA.35
2 PLIP interactions:2 interactions with chain B- Salt bridges: B:H.146, B:R.268
- 2 x HTO: HEPTANE-1,2,3-TRIOL(Non-covalent)
HTO.7: 3 residues within 4Å:- Chain A: Q.88, I.92, W.143
1 PLIP interactions:1 interactions with chain A- Hydrophobic interactions: A:I.92
HTO.34: 4 residues within 4Å:- Chain C: Q.205, S.206, N.207, R.208
4 PLIP interactions:4 interactions with chain C- Hydrophobic interactions: C:Q.205
- Hydrogen bonds: C:N.207, C:R.208, C:R.208
- 12 x GOL: GLYCEROL(Non-functional Binders)
GOL.8: 7 residues within 4Å:- Chain A: A.199, N.200, P.201
- Chain C: K.68, T.69, F.70
- Ligands: GOL.27
5 PLIP interactions:2 interactions with chain A, 3 interactions with chain C- Hydrogen bonds: A:P.201, C:T.69
- Water bridges: A:G.204, C:T.69, C:T.69
GOL.9: 3 residues within 4Å:- Chain A: A.79, G.85, Q.88
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:Q.88
GOL.10: 9 residues within 4Å:- Chain A: S.53, S.66, V.67, Y.68, L.81, A.82, G.84, L.86, W.87
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:S.66, A:Y.68, A:G.84, A:G.84, A:L.86, A:W.87
GOL.11: 4 residues within 4Å:- Chain A: P.62, I.65, Y.149, I.151
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:Y.149
GOL.12: 8 residues within 4Å:- Chain A: M.207, R.208, T.209, P.210
- Chain B: L.236, E.237
- Chain C: P.73, E.128
5 PLIP interactions:2 interactions with chain B, 1 interactions with chain A, 2 interactions with chain C- Hydrogen bonds: B:E.237, A:R.208, C:E.128, C:E.128
- Water bridges: B:L.236
GOL.14: 5 residues within 4Å:- Chain A: S.5, R.8
- Chain C: E.51, G.53, E.87
6 PLIP interactions:3 interactions with chain C, 3 interactions with chain A- Hydrogen bonds: C:E.49, A:R.8
- Water bridges: C:G.53, C:E.87, A:F.6, A:E.7
GOL.24: 4 residues within 4Å:- Chain A: P.29
- Chain B: M.257, G.258
- Ligands: LDA.30
No protein-ligand interaction detected (PLIP)GOL.27: 8 residues within 4Å:- Chain A: N.200
- Chain B: R.268
- Chain C: E.40, R.43, K.68
- Ligands: GOL.8, PO4.25, LDA.35
6 PLIP interactions:4 interactions with chain C, 2 interactions with chain B- Hydrogen bonds: C:R.43, C:K.68, B:R.268, B:R.268
- Water bridges: C:Y.36, C:E.40
GOL.28: 2 residues within 4Å:- Chain C: A.31, Y.35
No protein-ligand interaction detected (PLIP)GOL.29: 1 residues within 4Å:- Chain C: W.27
No protein-ligand interaction detected (PLIP)GOL.31: 11 residues within 4Å:- Chain B: S.228, R.229, F.230, G.231, R.234
- Chain C: R.183, F.184, P.198, Q.200, E.236, C.240
9 PLIP interactions:5 interactions with chain C, 4 interactions with chain B- Hydrogen bonds: C:R.183, C:R.183, C:Q.200, C:E.236, B:R.229, B:G.231, B:R.234
- Water bridges: C:E.236, B:F.230
GOL.33: 6 residues within 4Å:- Chain B: F.209, W.269, M.273
- Chain C: L.30, L.37
- Ligands: LDA.30
No protein-ligand interaction detected (PLIP)- 1 x FE: FE (III) ION(Non-covalent)
- 1 x SPO: SPHEROIDENE(Non-covalent)
SPO.21: 23 residues within 4Å:- Chain B: W.67, F.68, I.71, G.72, F.75, W.76, F.86, F.106, W.116, S.120, F.121, M.123, W.158, L.161, G.162, F.163, W.172, V.176, Y.178, G.179, I.180, H.183
- Ligands: BCL.16
19 PLIP interactions:19 interactions with chain B- Hydrophobic interactions: B:W.67, B:F.68, B:F.68, B:F.68, B:I.71, B:I.71, B:F.75, B:F.86, B:F.106, B:W.116, B:F.121, B:W.158, B:L.161, B:W.172, B:V.176, B:V.176, B:Y.178, B:Y.178, B:I.180
- 1 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)
- 1 x K: POTASSIUM ION(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Saer, R.G. et al., Role of Rhodobacter sphaeroides Photosynthetic Reaction Center Residue M214 in the Composition, Absorbance Properties, and Conformations of HA and BA Cofactors. Biochemistry (2013)
- Release Date
- 2013-05-01
- Peptides
- Reaction center protein L chain: A
Reaction center protein M chain: B
Reaction center protein H chain: C - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
LB
MC
H - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.20 Å
- Oligo State
- hetero-1-1-1-mer
- Ligands
- 6 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)
- 2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)
- 2 x U10: UBIQUINONE-10(Non-covalent)
- 4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)
- 3 x PO4: PHOSPHATE ION(Non-functional Binders)
- 2 x HTO: HEPTANE-1,2,3-TRIOL(Non-covalent)
- 12 x GOL: GLYCEROL(Non-functional Binders)
- 1 x FE: FE (III) ION(Non-covalent)
- 1 x SPO: SPHEROIDENE(Non-covalent)
- 1 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)
- 1 x K: POTASSIUM ION(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Saer, R.G. et al., Role of Rhodobacter sphaeroides Photosynthetic Reaction Center Residue M214 in the Composition, Absorbance Properties, and Conformations of HA and BA Cofactors. Biochemistry (2013)
- Release Date
- 2013-05-01
- Peptides
- Reaction center protein L chain: A
Reaction center protein M chain: B
Reaction center protein H chain: C - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
LB
MC
H - Membrane
-
We predict this structure to be a membrane protein.