- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.96 Å
- Oligo State
- hetero-1-1-1-1-mer
- Ligands
- 19 x SO4: SULFATE ION(Non-functional Binders)
- 4 x HEC: HEME C(Covalent)
HEC.8: 23 residues within 4Å:- Chain A: Y.56, K.57, N.58, V.59, K.60, V.61, L.62, F.70, M.74, T.75, I.77, T.78, S.82, G.86, C.87, C.90, H.91, L.96, A.97, Y.104, A.107, R.108
- Ligands: HEC.9
19 PLIP interactions:19 interactions with chain A,- Hydrophobic interactions: A:Y.56, A:V.59, A:F.70, A:F.70, A:M.74, A:I.77, A:L.96, A:A.107, A:R.108
- Hydrogen bonds: A:K.57, A:N.58, A:N.58, A:K.60, A:V.61, A:L.62
- Salt bridges: A:R.108
- pi-Stacking: A:F.70, A:Y.104
- Metal complexes: A:H.91
HEC.9: 24 residues within 4Å:- Chain A: I.77, V.81, Y.89, Y.102, P.103, V.106, M.110, L.111, M.113, T.114, T.131, C.132, C.135, H.136, P.140, L.141, P.142, V.145, L.282, L.289, R.293, P.301
- Ligands: HEC.8, HEC.11
13 PLIP interactions:13 interactions with chain A,- Hydrophobic interactions: A:I.77, A:V.81, A:P.103, A:V.106, A:M.110, A:L.111, A:V.145, A:L.282, A:P.301
- Hydrogen bonds: A:P.140
- Salt bridges: A:R.293, A:R.293
- Metal complexes: A:H.136
HEC.10: 25 residues within 4Å:- Chain A: V.201, R.202, V.203, V.204, T.229, F.230, M.233, M.234, I.236, S.237, T.242, N.243, C.244, C.247, H.248, F.253, E.254, R.264, A.267, W.268, I.271, R.272
- Chain C: Y.162
- Chain D: I.189
- Ligands: HEC.11
29 PLIP interactions:27 interactions with chain A, 1 interactions with chain D, 1 interactions with chain C,- Hydrophobic interactions: A:V.201, A:T.229, A:F.230, A:M.233, A:I.236, A:T.242, A:F.253, A:F.253, A:F.253, A:F.253, A:R.264, A:A.267, A:W.268, A:I.271, D:I.189, C:Y.162
- Hydrogen bonds: A:V.203, A:V.204, A:Q.206, A:E.254
- Water bridges: A:R.264, A:R.272, A:R.272, A:R.272, A:R.272
- Salt bridges: A:R.202, A:R.272
- pi-Cation interactions: A:R.264
- Metal complexes: A:H.248
HEC.11: 26 residues within 4Å:- Chain A: I.117, H.124, V.125, T.128, G.129, V.130, I.236, L.240, F.246, Q.263, I.266, A.267, G.270, I.271, M.273, V.274, D.304, C.305, C.308, H.309, T.313, K.314, P.315, G.318
- Ligands: HEC.9, HEC.10
18 PLIP interactions:18 interactions with chain A,- Hydrophobic interactions: A:I.117, A:V.125, A:V.125, A:V.130, A:I.236, A:I.266, A:A.267, A:I.271
- Hydrogen bonds: A:T.128, A:Q.263
- Water bridges: A:T.313, A:K.314, A:K.314
- Salt bridges: A:K.314, A:K.314
- pi-Stacking: A:H.309
- Metal complexes: A:H.124, A:H.309
- 5 x HTO: HEPTANE-1,2,3-TRIOL(Non-covalent)
HTO.12: 8 residues within 4Å:- Chain A: P.205, Q.206, T.207, L.209, P.210, L.211, V.214
- Chain D: D.290
7 PLIP interactions:5 interactions with chain A, 2 interactions with chain D- Hydrophobic interactions: A:L.211
- Hydrogen bonds: A:Q.206, A:T.207, A:T.207, A:L.211, D:D.290, D:D.290
HTO.13: 9 residues within 4Å:- Chain A: E.21, L.23, L.240, G.241, G.311, V.312, T.313, K.314, F.317
9 PLIP interactions:9 interactions with chain A- Hydrophobic interactions: A:V.312, A:K.314, A:F.317
- Hydrogen bonds: A:K.31, A:G.311, A:T.313, A:T.313
- Water bridges: A:G.241, A:T.242
HTO.20: 10 residues within 4Å:- Chain B: L.70, A.121, V.123, V.124, D.125, A.126, L.232
- Chain D: E.234, T.237, D.238
9 PLIP interactions:5 interactions with chain B, 4 interactions with chain D- Hydrophobic interactions: B:L.70, B:A.121, B:L.232, D:E.234, D:D.238
- Hydrogen bonds: B:D.125, B:A.126
- Water bridges: D:E.234, D:E.234
HTO.31: 5 residues within 4Å:- Chain C: Y.29
- Chain D: I.254, F.256
- Ligands: LDA.18, MQ9.27
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:Y.29, C:Y.29
HTO.32: 3 residues within 4Å:- Chain C: G.114, W.115
- Ligands: SO4.38
3 PLIP interactions:2 interactions with chain C, 1 interactions with chain D- Hydrophobic interactions: C:W.115
- Hydrogen bonds: C:W.115
- Water bridges: D:R.226
- 4 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)
LDA.18: 7 residues within 4Å:- Chain B: L.29, R.33
- Chain D: F.206, F.256, F.270
- Ligands: MQ9.27, HTO.31
5 PLIP interactions:5 interactions with chain D- Hydrophobic interactions: D:F.206, D:F.206, D:F.256, D:F.270
- pi-Cation interactions: D:F.256
LDA.19: 9 residues within 4Å:- Chain B: P.42, V.59, Y.60, L.62, P.63, Y.64, P.65, P.79, R.80
4 PLIP interactions:4 interactions with chain B- Hydrophobic interactions: B:P.42, B:Y.64, B:P.65
- pi-Cation interactions: B:Y.64
LDA.30: 13 residues within 4Å:- Chain B: W.17
- Chain C: D.60, F.62, L.151
- Chain D: Y.195, Y.196, C.197, P.198, G.201, C.296, H.299, A.301
- Ligands: BCB.25
7 PLIP interactions:2 interactions with chain B, 2 interactions with chain D, 3 interactions with chain C- Hydrophobic interactions: B:W.17, B:W.17, D:P.198, D:A.301, C:L.151
- Hydrogen bonds: C:D.60
- Salt bridges: C:D.60
LDA.47: 7 residues within 4Å:- Chain D: A.57, L.122, G.125, S.126, I.129, S.133
- Ligands: SO4.37
3 PLIP interactions:3 interactions with chain D- Hydrophobic interactions: D:A.57, D:L.122, D:I.129
- 6 x UNL: UNKNOWN LIGAND(Covalent)(Non-covalent)
UNL.21: 6 residues within 4Å:- Chain A: R.216
- Chain B: H.3, G.4, A.5
- Chain D: T.287, F.288
3 PLIP interactions:2 interactions with chain D, 1 interactions with chain B- Hydrophobic interactions: D:T.287, D:F.288, B:H.3
UNL.33: 4 residues within 4Å:- Chain C: W.59, P.61, I.64, Y.148
3 PLIP interactions:3 interactions with chain C- Hydrophobic interactions: C:W.59, C:I.64, C:Y.148
UNL.34: 6 residues within 4Å:- Chain C: P.171, M.174, S.175, S.178
- Ligands: UQ1.29, BCB.43
1 PLIP interactions:1 interactions with chain C- Hydrophobic interactions: C:M.174
UNL.35: 4 residues within 4Å:- Chain C: L.75, Q.87, T.90, W.142
3 PLIP interactions:3 interactions with chain C- Hydrophobic interactions: C:T.90, C:W.142, C:W.142
UNL.48: 4 residues within 4Å:- Chain D: F.71, N.72, A.75, W.112
4 PLIP interactions:4 interactions with chain D- Hydrophobic interactions: D:F.71, D:A.75, D:W.112, D:W.112
UNL.49: 5 residues within 4Å:- Chain B: W.21
- Chain C: F.62
- Chain D: P.198, F.202
- Ligands: BCB.25
1 PLIP interactions:1 interactions with chain C- Hydrophobic interactions: C:F.62
- 1 x FE2: FE (II) ION(Non-covalent)
- 4 x BCB: BACTERIOCHLOROPHYLL B(Non-covalent)
BCB.24: 32 residues within 4Å:- Chain C: F.97, P.124, I.125, M.127, F.128, L.131, V.157, N.158, F.160, G.161, Y.162, W.167, H.168, G.172, H.173, S.176, V.177, L.180, F.181, I.240, F.241, G.244, G.247, T.248
- Chain D: L.184, Y.195, Y.208
- Ligands: BCB.25, BPB.26, MQ9.27, BCB.43, BCB.44
20 PLIP interactions:20 interactions with chain C,- Hydrophobic interactions: C:F.97, C:F.97, C:P.124, C:F.128, C:V.157, C:F.160, C:Y.162, C:W.167, C:W.167, C:V.177, C:L.180, C:F.181, C:I.240, C:F.241, C:F.241
- Hydrogen bonds: C:S.176, C:T.248
- pi-Stacking: C:W.167, C:H.173
- Metal complexes: C:H.173
BCB.25: 22 residues within 4Å:- Chain C: I.49, F.97, F.128, F.146, I.150, L.151, H.153, L.154, V.157
- Chain D: Y.195, G.201, I.204, G.205, Y.208, G.209, L.212
- Ligands: BCB.24, BPB.26, MQ9.27, LDA.30, BCB.44, UNL.49
11 PLIP interactions:4 interactions with chain D, 7 interactions with chain C,- Hydrophobic interactions: D:Y.195, D:I.204, D:I.204, C:I.49, C:F.97, C:F.128, C:F.146, C:L.154, C:V.157
- pi-Stacking: D:Y.208
- Metal complexes: C:H.153
BCB.43: 23 residues within 4Å:- Chain C: H.168, M.174, V.177, S.178, F.181, V.182, M.185, V.220, Y.222
- Chain D: F.154, V.155, I.158, I.177, W.178, H.180, I.181, W.183, L.184
- Ligands: BCB.24, UNL.34, BCB.44, BPB.45, NS5.46
13 PLIP interactions:8 interactions with chain D, 5 interactions with chain C,- Hydrophobic interactions: D:F.154, D:V.155, D:I.158, D:I.177, D:I.181, D:W.183, D:L.184, C:V.177, C:F.181, C:M.185, C:V.220
- Metal complexes: D:H.180
- pi-Stacking: C:F.181
BCB.44: 32 residues within 4Å:- Chain C: V.157, Y.162, F.181
- Chain D: G.62, I.66, I.69, M.120, L.124, F.148, A.151, F.154, V.155, I.158, W.183, L.184, T.185, F.187, S.188, F.194, Y.195, H.200, S.203, I.204, A.207, Y.208, M.275, A.278, I.282
- Ligands: BCB.24, BCB.25, BCB.43, BPB.45
22 PLIP interactions:22 interactions with chain D,- Hydrophobic interactions: D:I.66, D:I.69, D:L.124, D:F.148, D:A.151, D:F.154, D:F.154, D:V.155, D:W.183, D:L.184, D:L.184, D:F.187, D:F.194, D:Y.195, D:Y.195, D:I.204, D:A.207, D:Y.208, D:A.278
- Hydrogen bonds: D:Y.195, D:S.203
- Metal complexes: D:H.200
- 2 x BPB: BACTERIOPHEOPHYTIN B(Non-covalent)
BPB.26: 29 residues within 4Å:- Chain C: F.41, I.42, I.49, A.93, A.96, F.97, W.100, E.104, V.117, A.120, F.121, P.124, F.128, Y.148, G.149, I.150, H.153, A.237, S.238, F.241
- Chain D: Y.208, G.211, L.212, A.215, W.250, I.254
- Ligands: BCB.24, BCB.25, MQ9.27
17 PLIP interactions:15 interactions with chain C, 2 interactions with chain D- Hydrophobic interactions: C:I.42, C:I.42, C:I.49, C:A.96, C:A.120, C:F.121, C:F.121, C:F.121, C:F.121, C:F.128, C:Y.148, C:Y.148, C:F.241, C:F.241, D:Y.208, D:A.215
- Hydrogen bonds: C:E.104
BPB.45: 22 residues within 4Å:- Chain C: F.181, A.184, M.185, L.189, V.220
- Chain D: A.58, F.59, S.63, I.66, S.123, L.124, W.127, V.131, I.144, N.147, F.148, A.151, S.271, V.274, M.275
- Ligands: BCB.43, BCB.44
15 PLIP interactions:5 interactions with chain C, 10 interactions with chain D- Hydrophobic interactions: C:F.181, C:A.184, C:M.185, C:L.189, D:A.58, D:F.59, D:F.59, D:I.66, D:W.127, D:N.147, D:F.148, D:F.148, D:V.274
- Water bridges: C:Y.215
- pi-Stacking: D:F.148
- 1 x MQ9: MENAQUINONE-9(Non-covalent)
MQ9.27: 30 residues within 4Å:- Chain C: Y.29, F.30, G.35, I.39, I.42, F.43, V.46, W.100, R.103
- Chain D: L.213, H.217, T.220, V.243, A.246, A.247, W.250, I.254, F.256, N.257, A.258, T.259, I.260, V.263, W.266, F.270
- Ligands: LDA.18, BCB.24, BCB.25, BPB.26, HTO.31
22 PLIP interactions:9 interactions with chain C, 13 interactions with chain D- Hydrophobic interactions: C:Y.29, C:Y.29, C:Y.29, C:I.39, C:I.39, C:I.42, C:V.46, C:W.100, C:W.100, D:L.213, D:A.246, D:W.250, D:I.254, D:I.254, D:F.256, D:F.256, D:I.260, D:V.263, D:W.266, D:W.266, D:F.270
- Hydrogen bonds: D:A.258
- 2 x UQ1: UBIQUINONE-1(Non-covalent)
UQ1.28: 13 residues within 4Å:- Chain C: L.189, H.190, L.193, I.194, E.212, N.213, F.216, Y.222, S.223, I.224, G.225, A.226, I.229
8 PLIP interactions:8 interactions with chain C- Hydrophobic interactions: C:L.189, C:L.193, C:F.216, C:F.216, C:I.224, C:I.229
- Hydrogen bonds: C:I.224, C:G.225
UQ1.29: 6 residues within 4Å:- Chain C: W.263, W.266
- Chain D: F.85, F.88, F.89
- Ligands: UNL.34
7 PLIP interactions:4 interactions with chain C, 3 interactions with chain D- Hydrophobic interactions: C:W.263, C:W.266, C:W.266, D:F.89, D:F.89
- pi-Stacking: C:W.266
- Hydrogen bonds: D:F.89
- 1 x NS5: 15-cis-1,2-dihydroneurosporene(Non-covalent)
NS5.46: 18 residues within 4Å:- Chain D: I.66, I.69, L.70, F.88, G.117, L.118, T.121, V.155, G.159, C.160, W.169, V.173, P.174, F.175, G.176, I.177, H.180
- Ligands: BCB.43
13 PLIP interactions:13 interactions with chain D- Hydrophobic interactions: D:I.66, D:I.66, D:I.69, D:L.70, D:F.88, D:W.169, D:V.173, D:V.173, D:F.175, D:F.175, D:F.175, D:I.177, D:H.180
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Li, L. et al., Nanoliter microfluidic hybrid method for simultaneous screening and optimization validated with crystallization of membrane proteins. Proc.Natl.Acad.Sci.Usa (2006)
- Release Date
- 2006-09-19
- Peptides
- Photosynthetic reaction center cytochrome c subunit: A
Reaction center protein H chain: B
Reaction center protein L chain: C
Reaction center protein M chain: D - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
CB
HC
LD
M - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.96 Å
- Oligo State
- hetero-1-1-1-1-mer
- Ligands
- 19 x SO4: SULFATE ION(Non-functional Binders)
- 4 x HEC: HEME C(Covalent)
- 5 x HTO: HEPTANE-1,2,3-TRIOL(Non-covalent)
- 4 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)
- 6 x UNL: UNKNOWN LIGAND(Covalent)(Non-covalent)
- 1 x FE2: FE (II) ION(Non-covalent)
- 4 x BCB: BACTERIOCHLOROPHYLL B(Non-covalent)
- 2 x BPB: BACTERIOPHEOPHYTIN B(Non-covalent)
- 1 x MQ9: MENAQUINONE-9(Non-covalent)
- 2 x UQ1: UBIQUINONE-1(Non-covalent)
- 1 x NS5: 15-cis-1,2-dihydroneurosporene(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Li, L. et al., Nanoliter microfluidic hybrid method for simultaneous screening and optimization validated with crystallization of membrane proteins. Proc.Natl.Acad.Sci.Usa (2006)
- Release Date
- 2006-09-19
- Peptides
- Photosynthetic reaction center cytochrome c subunit: A
Reaction center protein H chain: B
Reaction center protein L chain: C
Reaction center protein M chain: D - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
CB
HC
LD
M - Membrane
-
We predict this structure to be a membrane protein.