- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.01 Å
- Oligo State
- hetero-1-1-1-mer
- Ligands
- 4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)
- 2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)
BPH.3: 32 residues within 4Å:- Chain A: T.38, F.41, 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, F.146, Y.148, G.149, I.150, H.153, L.238, V.241
- Chain B: Y.210, A.213, L.214, M.218, W.252, T.255, M.256
- Ligands: BCL.1, BCL.2, U10.40
17 PLIP interactions:15 interactions with chain A, 2 interactions with chain B- Hydrophobic interactions: A:I.49, A:A.96, A:A.120, A:F.121, A:F.121, A:F.123, A:A.124, A:Y.128, A:F.146, A:Y.148, A:L.238, A:V.241, A:V.241, B:Y.210, B:A.213
- Hydrogen bonds: A:E.104
- pi-Stacking: A:F.121
BPH.38: 26 residues within 4Å:- Chain A: F.181, A.184, L.185, L.189, F.216, L.219, V.220
- Chain B: 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, T.277
- Ligands: U10.4, BCL.36, BCL.37, LDA.57
13 PLIP interactions:2 interactions with chain A, 11 interactions with chain B- Hydrophobic interactions: A:A.184, A:L.189, B:L.60, B:L.64, B:W.66, B:F.67, B:W.129, B:A.149, B:F.150, B:F.150, B:A.153, B:T.277
- pi-Stacking: B:F.150
- 2 x U10: UBIQUINONE-10(Non-covalent)
U10.4: 28 residues within 4Å:- Chain A: M.174, S.178, F.179, T.182, A.186, 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
- Chain B: W.66, F.67, L.89, F.90
- Ligands: UQ1.5, LDA.33, BCL.36, BCL.37, BPH.38, SPO.41
15 PLIP interactions:11 interactions with chain A, 4 interactions with chain B- Hydrophobic interactions: A:F.179, A:F.179, A:T.182, A:A.186, A:L.189, A:L.193, A:I.224, A:I.229, A:I.229, B:W.66, B:L.89, B:F.90, B:F.90
- Hydrogen bonds: A:I.224, A:G.225
U10.40: 26 residues within 4Å:- Chain A: V.26, Y.30, G.35, F.39, W.100, R.103
- Chain B: 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, M.262, I.265, W.268, M.272
- Ligands: BCL.2, BPH.3, LDA.25
17 PLIP interactions:13 interactions with chain B, 4 interactions with chain A- Hydrophobic interactions: B:L.214, B:M.218, B:H.219, B:W.252, B:M.256, B:F.258, B:F.258, B:A.260, B:I.265, B:I.265, B:W.268, B:W.268, A:V.26, A:F.39, A:W.100, A:W.100
- Hydrogen bonds: B:A.260
- 1 x UQ1: UBIQUINONE-1(Non-covalent)
- 7 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.6: 4 residues within 4Å:- Chain A: E.72, Y.73, K.82
- Ligands: GOL.17
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:E.72, A:Y.73
- Salt bridges: A:K.82
PO4.7: 6 residues within 4Å:- Chain A: F.24, W.25, V.26
- Chain C: E.94, G.95, F.96
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:W.25
PO4.8: 6 residues within 4Å:- Chain A: Y.162, G.165, N.166
- Chain B: N.187, L.191
- Ligands: GOL.46
4 PLIP interactions:3 interactions with chain A, 1 interactions with chain B- Hydrogen bonds: A:N.166, B:N.187
- Water bridges: A:G.165, A:N.166
PO4.9: 4 residues within 4Å:- Chain A: M.139, G.140, A.141, Y.144
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:Y.144, A:Y.144
PO4.44: 4 residues within 4Å:- Chain B: N.25, N.28, G.53, S.54
11 PLIP interactions:11 interactions with chain B- Hydrogen bonds: B:N.25, B:S.54, B:S.54
- Water bridges: B:N.28, B:N.28, B:Y.51, B:Y.51, B:S.54, B:S.54, B:S.54, B:L.55
PO4.45: 6 residues within 4Å:- Chain B: E.173, W.185, N.188, F.189, H.193
- Ligands: GOL.48
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:E.173, B:W.185, B:W.185
- Water bridges: B:N.188
PO4.59: 5 residues within 4Å:- Chain C: K.146, V.198, Q.199, S.200
- Ligands: GOL.68
2 PLIP interactions:2 interactions with chain C- Water bridges: C:K.146, C:K.146
- 1 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)
- 26 x GOL: GLYCEROL(Non-functional Binders)
GOL.11: 8 residues within 4Å:- Chain A: S.52, L.55, S.65, V.66, Y.67, L.80, A.81, L.85
Ligand excluded by PLIPGOL.12: 5 residues within 4Å:- Chain A: A.198, N.199, P.200
- Chain C: T.63, F.64
Ligand excluded by PLIPGOL.13: 8 residues within 4Å:- Chain A: R.109, G.112, I.113, G.114, Y.115
- Chain B: E.2, R.228
- Chain C: L.241
Ligand excluded by PLIPGOL.14: 8 residues within 4Å:- Chain A: E.205, M.206, R.207, T.208, H.211
- Chain B: E.22
- Chain C: P.67, G.125
Ligand excluded by PLIPGOL.15: 2 residues within 4Å:- Chain A: N.60
- Ligands: HT3.23
Ligand excluded by PLIPGOL.16: 3 residues within 4Å:- Chain A: D.261, W.265
- Ligands: GOL.20
Ligand excluded by PLIPGOL.17: 3 residues within 4Å:- Chain A: E.72, Y.73
- Ligands: PO4.6
Ligand excluded by PLIPGOL.18: 6 residues within 4Å:- Chain A: G.77, A.78, G.84, Q.87, I.88
- Ligands: LDA.29
Ligand excluded by PLIPGOL.19: 1 residues within 4Å:- Chain A: Y.67
Ligand excluded by PLIPGOL.20: 6 residues within 4Å:- Chain A: W.255, W.262, W.265
- Ligands: DIO.10, GOL.16, LDA.33
Ligand excluded by PLIPGOL.21: 3 residues within 4Å:- Chain A: P.12, N.20
- Chain C: T.90
Ligand excluded by PLIPGOL.22: 4 residues within 4Å:- Chain A: Y.115, H.116, F.119
- Chain B: Q.4
Ligand excluded by PLIPGOL.46: 3 residues within 4Å:- Chain A: Y.162
- Chain B: L.191
- Ligands: PO4.8
Ligand excluded by PLIPGOL.47: 4 residues within 4Å:- Chain B: L.18, S.30, G.31, P.49
Ligand excluded by PLIPGOL.48: 4 residues within 4Å:- Chain B: S.172, E.173
- Ligands: PO4.45, GOL.50
Ligand excluded by PLIPGOL.49: 6 residues within 4Å:- Chain B: E.2, Y.3, Q.4, N.5, I.6, F.7
Ligand excluded by PLIPGOL.50: 7 residues within 4Å:- Chain B: E.95, P.96, P.97, A.98, P.99, S.172
- Ligands: GOL.48
Ligand excluded by PLIPGOL.60: 10 residues within 4Å:- Chain B: S.227, R.228, G.230, R.233
- Chain C: R.177, F.178, P.192, Q.194, E.230, C.234
Ligand excluded by PLIPGOL.61: 3 residues within 4Å:- Chain C: N.44, T.48, P.49
Ligand excluded by PLIPGOL.62: 3 residues within 4Å:- Chain A: P.12, G.13
- Chain C: M.242
Ligand excluded by PLIPGOL.63: 3 residues within 4Å:- Chain C: Q.199, R.202
- Ligands: GOL.68
Ligand excluded by PLIPGOL.64: 7 residues within 4Å:- Chain B: R.241
- Chain C: E.38, T.74, V.75, G.77, P.78, E.79
Ligand excluded by PLIPGOL.65: 4 residues within 4Å:- Chain C: I.160, A.161, S.210
- Ligands: HTO.69
Ligand excluded by PLIPGOL.66: 3 residues within 4Å:- Chain C: H.128, N.129, K.132
Ligand excluded by PLIPGOL.67: 5 residues within 4Å:- Chain B: A.1
- Chain C: R.154, K.197, Q.199, H.204
Ligand excluded by PLIPGOL.68: 6 residues within 4Å:- Chain C: Q.199, S.200, N.201, R.202
- Ligands: PO4.59, GOL.63
Ligand excluded by PLIP- 1 x HT3: (2R,3S)-heptane-1,2,3-triol(Non-covalent)
- 2 x HTO: HEPTANE-1,2,3-TRIOL(Non-covalent)
HTO.24: 5 residues within 4Å:- Chain A: I.46, I.49, W.59, I.64
- Ligands: LDA.26
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:W.59, A:I.64
HTO.69: 7 residues within 4Å:- Chain C: I.160, G.162, K.163, E.182, L.183, K.184
- Ligands: GOL.65
3 PLIP interactions:3 interactions with chain C- Hydrophobic interactions: C:K.184, C:K.184
- Hydrogen bonds: C:E.182
- 21 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)
LDA.25: 6 residues within 4Å:- Chain A: P.28
- Chain B: M.256, G.257, F.258
- Ligands: U10.40, LDA.70
Ligand excluded by PLIPLDA.26: 7 residues within 4Å:- Chain A: P.61, I.64, Y.148, G.149
- Ligands: BCL.2, HTO.24, LDA.71
Ligand excluded by PLIPLDA.27: 6 residues within 4Å:- Chain A: A.101, R.109, Y.115, P.118, F.119
- Ligands: LDA.32
Ligand excluded by PLIPLDA.28: 6 residues within 4Å:- Chain A: G.77, Q.87, T.90, I.91, L.133, W.142
Ligand excluded by PLIPLDA.29: 4 residues within 4Å:- Chain A: L.44, I.88, I.91
- Ligands: GOL.18
Ligand excluded by PLIPLDA.30: 3 residues within 4Å:- Chain A: I.254
- Ligands: DIO.10, LDA.33
Ligand excluded by PLIPLDA.31: 6 residues within 4Å:- Chain A: V.220, G.221
- Chain B: S.30, G.33
- Ligands: BCL.36, LDA.57
Ligand excluded by PLIPLDA.32: 8 residues within 4Å:- Chain A: F.119, A.122, F.123, L.126, V.241, F.242, A.245
- Ligands: LDA.27
Ligand excluded by PLIPLDA.33: 6 residues within 4Å:- Chain A: M.174, W.265
- Ligands: U10.4, GOL.20, LDA.30, BCL.36
Ligand excluded by PLIPLDA.34: 2 residues within 4Å:- Chain A: W.271
- Ligands: UQ1.5
Ligand excluded by PLIPLDA.35: 7 residues within 4Å:- Chain A: F.123, L.234, L.235, L.238, S.239, F.242
- Chain B: I.6
Ligand excluded by PLIPLDA.52: 12 residues within 4Å:- Chain A: W.151
- Chain B: P.200, L.204, A.207, F.208, W.268, M.272
- Chain C: L.24, L.31
- Ligands: BCL.2, LDA.70, LDA.73
Ligand excluded by PLIPLDA.53: 5 residues within 4Å:- Chain B: F.7, L.38, L.39, W.41, F.42
Ligand excluded by PLIPLDA.54: 6 residues within 4Å:- Chain B: L.167, M.168, L.285, G.288, T.289
- Chain C: L.12
Ligand excluded by PLIPLDA.55: 4 residues within 4Å:- Chain B: F.105, A.107, G.113, F.120
Ligand excluded by PLIPLDA.56: 5 residues within 4Å:- Chain B: W.127, S.128, G.131, Y.134, Q.138
Ligand excluded by PLIPLDA.57: 6 residues within 4Å:- Chain A: V.220
- Chain B: I.50, W.129
- Ligands: LDA.31, BCL.37, BPH.38
Ligand excluded by PLIPLDA.70: 10 residues within 4Å:- Chain B: R.253, F.258, W.268
- Chain C: Q.32, Y.40, Q.53, F.56
- Ligands: LDA.25, LDA.52, LDA.73
Ligand excluded by PLIPLDA.71: 3 residues within 4Å:- Chain C: W.21
- Ligands: LDA.26, LDA.73
Ligand excluded by PLIPLDA.72: 4 residues within 4Å:- Chain C: A.25, I.28, Y.29
- Ligands: LDA.73
Ligand excluded by PLIPLDA.73: 8 residues within 4Å:- Chain C: Y.18, W.21, A.25, I.28
- Ligands: LDA.52, LDA.70, LDA.71, LDA.72
Ligand excluded by PLIP- 1 x FE: FE (III) ION(Non-covalent)
- 1 x SPO: SPHEROIDENE(Non-covalent)
SPO.41: 22 residues within 4Å:- Chain B: F.67, 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: U10.4, BCL.36
18 PLIP interactions:18 interactions with chain B- Hydrophobic interactions: B:F.67, B:F.67, B:F.67, B:I.70, B:I.70, B:F.74, B:F.85, B:W.115, B:F.120, B:W.157, B:L.160, B:F.162, B:F.162, B:W.171, B:V.175, B:V.175, B:Y.177, B:I.179
- 2 x K: POTASSIUM ION(Non-covalent)
K.42: 2 residues within 4Å:- Chain B: V.192, D.292
2 PLIP interactions:2 interactions with chain B- Metal complexes: B:V.192, B:D.292
K.58: 3 residues within 4Å:- Chain C: M.134, A.137, F.140
5 PLIP interactions:3 interactions with chain C, 2 Ligand-Water interactions- Metal complexes: C:M.134, C:A.137, C:F.140, H2O.15, H2O.15
- 1 x CL: CHLORIDE ION(Non-functional Binders)
- 1 x CDL: CARDIOLIPIN(Non-covalent)
CDL.51: 18 residues within 4Å:- Chain A: N.199, P.200
- Chain B: G.143, K.144, H.145, W.148, W.155, R.267, I.270, W.271, L.278
- Chain C: F.20, I.22, F.23, G.26, L.27, Y.30
- Ligands: CL.43
23 PLIP interactions:1 interactions with chain A, 16 interactions with chain B, 6 interactions with chain C- Hydrogen bonds: A:N.199, B:K.144, B:R.267
- Hydrophobic interactions: B:W.148, B:W.148, B:W.148, B:W.148, B:W.148, B:W.155, B:I.270, B:W.271, B:L.278, C:I.22, C:F.23, C:L.27, C:Y.30
- Water bridges: B:K.144, C:K.62, C:K.62
- Salt bridges: B:H.145, B:H.145, B:H.145, B:R.267
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Fujii, R. et al., Structure of the carotenoid bound to the reaction centre from Rhodobacter sphaeroides 2.4.1 revealed by time-resolved X-ray crystallography. To be Published
- Release Date
- 2010-12-01
- 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.
SMTL ID : 3i4d.1
Photosynthetic reaction center from rhodobacter sphaeroides 2.4.1
Reaction center protein L chain
Reaction center protein M chain
Reaction center protein H chain
Related Entries With Identical Sequence
1aig.1 | 1aig.2 | 1aij.1 | 1aij.2 | 1ds8.1 | 1ds8.2 | 1dv3.1 | 1dv3.2 | 1dv6.1 | 1dv6.2 | 1e14.1 | 1e6d.1 | 1f6n.1 | 1fnp.1 | 1fnq.1 | 1jgw.1 | 1jgx.1 | 1jgy.1 | 1jgz.1 | 1jh0.1 | 1k6l.1 | 1k6n.1 | 1kby.1 | 1l9b.1 | 1l9j.1 | 1l9j.2 | 1m3x.1 | 1mps.1 | 1ogv.1 | 1pcr.1 more...less...1qov.1 | 1rg5.1 | 1rgn.1 | 1rqk.1 | 1ry5.1 | 1rzh.1 | 1rzz.1 | 1rzz.2 | 1s00.1 | 1s00.2 | 1umx.1 | 1yf6.1 | 1yst.1 | 1z9j.1 | 1z9k.1 | 1z9k.2 | 2bnp.1 | 2bns.1 | 2boz.1 | 2gmr.1 | 2gnu.1 | 2hg3.1 | 2hg9.1 | 2hh1.1 | 2hhk.1 | 2hit.1 | 2hj6.1 | 2j8c.1 | 2j8d.1 | 2jiy.1 | 2jj0.1 | 2rcr.1 | 2uws.1 | 2uwt.1 | 2uwu.1 | 2uwv.1 | 2uww.1 | 2ux3.1 | 2ux4.1 | 2ux5.1 | 2uxj.1 | 2uxk.1 | 2uxl.1 | 2uxm.1 | 2wx5.1 | 3dsy.1 | 3dta.1 | 3dtr.1 | 3dts.1 | 3du2.1 | 3du3.1 | 3duq.1 | 3zum.1 | 3zuw.1 | 4h99.1 | 4h9l.1 | 4hbh.1 | 4hbj.1 | 4in6.1 | 4lwy.1 | 4n7k.1 | 4n7l.1 | 4rcr.1 | 4tqq.1 | 4v9g.30 | 4v9g.62 | 5lri.1 | 5lse.1 | 7pil.1 | 7pqd.30 | 7pqd.31 | 7pqd.65 | 7pqd.66 | 7va9.3 | 7va9.35 | 7vb9.1 | 7vnm.1 | 7vny.1 | 7vor.3 | 7vor.36 | 7vot.3 | 7vot.36 | 7voy.1 | 8vtj.1 | 8vtk.1 | 8vtl.1 | 8vtm.1 | 8vtn.1 | 8vto.1