- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.40 Å
- Oligo State
- hetero-1-1-1-1-mer
- Ligands
- 4 x HEC: HEME C(Covalent)
- 6 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)
LDA.5: 11 residues within 4Å:- Chain B: R.34, Y.41, P.42, V.59, Y.60, L.62, Y.64, P.65, P.79, R.80, R.81
4 PLIP interactions:4 interactions with chain B- Hydrophobic interactions: B:Y.64, B:P.65
- Water bridges: B:R.34
- pi-Cation interactions: B:Y.64
LDA.17: 8 residues within 4Å:- Chain B: L.29, R.33
- Chain D: F.202, G.205, F.206, F.256
- Ligands: MQ7.15, LDA.20
3 PLIP interactions:3 interactions with chain D- Hydrophobic interactions: D:F.206, D:F.256
- pi-Cation interactions: D:F.256
LDA.18: 15 residues within 4Å:- Chain B: Q.14, W.17, Y.18
- Chain C: F.62, L.151
- Chain D: Y.195, Y.196, C.197, P.198, G.201, W.295, C.296, H.299, A.301
- Ligands: BCB.8
9 PLIP interactions:2 interactions with chain C, 4 interactions with chain D, 3 interactions with chain B- Hydrophobic interactions: C:F.62, C:L.151, D:P.198, D:W.295, D:H.299, D:A.301, B:W.17, B:W.17, B:W.17
LDA.19: 9 residues within 4Å:- Chain D: W.23, A.53, S.54, A.57, L.122, S.126, I.129, S.133
- Ligands: SO4.24
3 PLIP interactions:3 interactions with chain D- Hydrophobic interactions: D:A.53, D:A.57
- Hydrogen bonds: D:W.23
LDA.20: 6 residues within 4Å:- Chain C: P.28, Y.29
- Chain D: I.254, G.255, F.256
- Ligands: LDA.17
No protein-ligand interaction detected (PLIP)LDA.21: 5 residues within 4Å:- Chain D: F.71, N.72, A.75, H.108, W.112
3 PLIP interactions:3 interactions with chain D- Hydrophobic interactions: D:F.71, D:A.75, D:W.112
- 4 x SO4: SULFATE ION(Non-functional Binders)
SO4.6: 6 residues within 4Å:- Chain B: R.33, R.37, Y.41, L.43, E.61
- Chain D: R.251
7 PLIP interactions:5 interactions with chain B, 2 interactions with chain D- Hydrogen bonds: B:R.33, B:Y.41
- Water bridges: B:R.37, B:Y.41, D:R.251
- Salt bridges: B:R.37, D:R.251
SO4.22: 3 residues within 4Å:- Chain C: N.199
- Chain D: H.143, R.265
3 PLIP interactions:1 interactions with chain C, 2 interactions with chain D- Hydrogen bonds: C:N.199
- Salt bridges: D:H.143, D:R.265
SO4.23: 3 residues within 4Å:- Chain B: L.246
- Chain D: A.1, R.226
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:A.1
- Water bridges: D:D.2, D:R.226
- Salt bridges: D:R.226
SO4.24: 7 residues within 4Å:- Chain D: W.23, Y.50, G.52, A.53, S.54, S.133
- Ligands: LDA.19
8 PLIP interactions:8 interactions with chain D- Hydrogen bonds: D:A.53, D:S.54, D:S.54, D:S.133
- Water bridges: D:W.23, D:G.55, D:G.55, D:R.134
- 4 x BCB: BACTERIOCHLOROPHYLL B(Non-covalent)
BCB.7: 29 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, H.173, S.176, V.177, L.180, F.181, I.240, F.241, G.244, T.248
- Chain D: L.184, Y.195, Y.208
- Ligands: BCB.8, BPB.9, BCB.11, BCB.12
17 PLIP interactions:17 interactions with chain C,- Hydrophobic interactions: C:F.97, C:P.124, 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
- Metal complexes: C:H.173
BCB.8: 20 residues within 4Å:- Chain C: I.49, F.128, F.146, I.150, H.153, L.154, V.157
- Chain D: Y.195, G.201, I.204, G.205, Y.208, G.209, L.212, F.270
- Ligands: BCB.7, BPB.9, BCB.12, MQ7.15, LDA.18
12 PLIP interactions:7 interactions with chain C, 5 interactions with chain D,- Hydrophobic interactions: C:I.49, C:F.128, C:F.146, C:F.146, C:L.154, C:V.157, D:Y.195, D:I.204, D:I.204, D:F.270
- Metal complexes: C:H.153
- pi-Stacking: D:Y.208
BCB.11: 21 residues within 4Å:- Chain C: H.168, M.174, V.177, S.178, F.181, V.182, V.220
- Chain D: F.154, V.155, I.158, I.177, W.178, H.180, I.181, W.183, L.184
- Ligands: BCB.7, SMA.10, BCB.12, BPB.13, NS5.16
11 PLIP interactions:7 interactions with chain D, 4 interactions with chain C,- Hydrophobic interactions: D:F.154, D:V.155, D:I.158, D:I.181, D:W.183, D:L.184, C:V.177, C:V.182
- Metal complexes: D:H.180
- pi-Stacking: C:F.181, C:F.181
BCB.12: 30 residues within 4Å:- Chain C: V.157, Y.162, F.181
- Chain D: G.62, I.66, I.69, 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.7, BCB.8, BCB.11, BPB.13
21 PLIP interactions:21 interactions with chain D,- Hydrophobic interactions: D:I.66, D:I.69, D:F.148, D:A.151, D:F.154, D:F.154, D:F.154, D:V.155, D:W.183, D:L.184, D:F.187, D:F.194, D:Y.195, D:Y.195, D:I.204, D:A.207, D:Y.208
- Hydrogen bonds: D:Y.195, D:S.203
- Salt bridges: D:H.200
- Metal complexes: D:H.200
- 2 x BPB: BACTERIOPHEOPHYTIN B(Non-covalent)
BPB.9: 27 residues within 4Å:- Chain C: F.41, I.42, G.45, I.49, A.96, F.97, W.100, E.104, V.117, A.120, F.121, V.123, P.124, Y.148, G.149, I.150, H.153, A.237, F.241
- Chain D: Y.208, G.211, L.212, W.250, I.254
- Ligands: BCB.7, BCB.8, MQ7.15
14 PLIP interactions:13 interactions with chain C, 1 interactions with chain D- Hydrophobic interactions: C:I.42, C:I.42, C:I.49, C:A.120, C:F.121, C:F.121, C:F.121, C:V.123, C:P.124, C:Y.148, C:Y.148, C:F.241, D:Y.208
- Hydrogen bonds: C:E.104
BPB.13: 20 residues within 4Å:- Chain C: F.181, 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, S.271, M.275
- Ligands: SMA.10, BCB.11, BCB.12
10 PLIP interactions:2 interactions with chain C, 8 interactions with chain D- Hydrophobic interactions: C:F.181, C:L.189, D:F.59, D:I.66, D:W.127, D:N.147, D:F.148, D:F.148, D:F.148, D:F.148
- 1 x SMA: STIGMATELLIN A(Non-covalent)
SMA.10: 18 residues within 4Å:- Chain C: A.186, L.189, H.190, L.193, I.194, E.212, N.213, F.216, V.220, Y.222, S.223, I.224, G.225, A.226, I.229, L.232
- Ligands: BCB.11, BPB.13
11 PLIP interactions:11 interactions with chain C- Hydrophobic interactions: C:L.189, C:F.216, C:F.216, C:V.220, C:Y.222, C:I.229, C:I.229, C:L.232
- Hydrogen bonds: C:S.223, C:I.224, C:G.225
- 1 x FE: FE (III) ION(Non-covalent)
- 1 x MQ7: MENAQUINONE-7(Non-covalent)
MQ7.15: 25 residues within 4Å:- Chain C: Y.29, G.35, I.39, I.42, W.100, R.103
- Chain D: L.212, A.216, H.217, T.220, 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: BCB.8, BPB.9, LDA.17
22 PLIP interactions:14 interactions with chain D, 8 interactions with chain C- Hydrophobic interactions: D:L.212, D:A.216, D:T.220, D:A.246, D:W.250, D:I.254, D:F.256, D:F.256, D:I.260, D:V.263, D:W.266, D:W.266, D:F.270, C:Y.29, C:Y.29, C:Y.29, C:I.39, C:I.42, C:W.100, C:W.100, C:W.100
- Hydrogen bonds: D:A.258
- 1 x NS5: 15-cis-1,2-dihydroneurosporene(Non-covalent)
NS5.16: 16 residues within 4Å:- Chain D: I.66, F.88, L.114, G.117, M.120, T.121, G.159, C.160, W.169, V.173, P.174, F.175, G.176, I.177, H.180
- Ligands: BCB.11
11 PLIP interactions:11 interactions with chain D- Hydrophobic interactions: D:I.66, D:F.88, D:L.114, 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
- Lancaster, C.R.D. et al., A Comparison of Stigmatellin Conformations, Free and Bound to the Photosynthetic Reaction Center and the Cytochrome Bc(1) Complex. J.Mol.Biol. (2007)
- Release Date
- 2007-03-13
- 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 2.40 Å
- Oligo State
- hetero-1-1-1-1-mer
- Ligands
- 4 x HEC: HEME C(Covalent)
- 6 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)
- 4 x SO4: SULFATE ION(Non-functional Binders)
- 4 x BCB: BACTERIOCHLOROPHYLL B(Non-covalent)
- 2 x BPB: BACTERIOPHEOPHYTIN B(Non-covalent)
- 1 x SMA: STIGMATELLIN A(Non-covalent)
- 1 x FE: FE (III) ION(Non-covalent)
- 1 x MQ7: MENAQUINONE-7(Non-covalent)
- 1 x NS5: 15-cis-1,2-dihydroneurosporene(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Lancaster, C.R.D. et al., A Comparison of Stigmatellin Conformations, Free and Bound to the Photosynthetic Reaction Center and the Cytochrome Bc(1) Complex. J.Mol.Biol. (2007)
- Release Date
- 2007-03-13
- 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.