- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 3.50 Å
- Oligo State
- hetero-1-1-1-1-mer
- Ligands
- 4 x HEC: HEME C(Covalent)
- 1 x DGA: DIACYL GLYCEROL(Covalent)
- 4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)
BCL.6: 23 residues within 4Å:- Chain B: H.169, M.175, V.178, S.179, F.182, V.183, M.186
- Chain C: M.121, F.155, V.156, I.159, I.178, W.179, H.181, I.182, W.184, L.185
- Ligands: DGA.5, BCL.7, BCL.13, BPB.14, NS5.16, MPG.18
12 PLIP interactions:9 interactions with chain C, 3 interactions with chain B,- Hydrophobic interactions: C:F.155, C:V.156, C:I.159, C:I.178, C:I.182, C:W.184, C:L.185, C:L.185, B:V.178, B:F.182
- Metal complexes: C:H.181
- pi-Stacking: B:F.182
BCL.7: 31 residues within 4Å:- Chain B: F.98, F.122, P.125, I.126, M.128, F.129, L.132, V.158, N.159, F.161, Y.163, W.168, H.169, G.173, H.174, S.177, V.178, L.181, F.182, I.241, F.242, G.245, T.249
- Chain C: L.185, Y.196, Y.209
- Ligands: BCL.6, BCL.8, BPB.9, BCL.13, MQ7.15
17 PLIP interactions:17 interactions with chain B,- Hydrophobic interactions: B:F.98, B:F.122, B:P.125, B:F.161, B:Y.163, B:W.168, B:W.168, B:V.178, B:L.181, B:F.182, B:I.241, B:F.242, B:F.242
- Hydrogen bonds: B:S.177, B:T.249
- pi-Stacking: B:W.168
- Metal complexes: B:H.174
BCL.8: 20 residues within 4Å:- Chain B: I.50, F.129, L.132, F.147, I.151, H.154, L.155, V.158
- Chain C: Y.196, G.202, I.205, G.206, Y.209, G.210, L.213
- Ligands: BCL.7, BPB.9, BCL.13, MQ7.15, OTP.17
15 PLIP interactions:6 interactions with chain C, 9 interactions with chain B,- Hydrophobic interactions: C:Y.196, C:I.205, C:I.205, C:Y.209, C:L.213, B:I.50, B:F.129, B:L.132, B:L.132, B:F.147, B:L.155, B:V.158
- pi-Stacking: C:Y.209, B:H.154
- Metal complexes: B:H.154
BCL.13: 31 residues within 4Å:- Chain B: V.158, H.169, F.182
- Chain C: G.63, I.67, I.70, M.121, L.125, F.149, A.152, F.155, V.156, I.159, W.184, L.185, T.186, F.188, F.195, Y.196, H.201, S.204, I.205, A.208, Y.209, M.276, A.279, I.283
- Ligands: BCL.6, BCL.7, BCL.8, BPB.14
17 PLIP interactions:17 interactions with chain C,- Hydrophobic interactions: C:I.67, C:I.70, C:L.125, C:F.149, C:A.152, C:F.155, C:V.156, C:W.184, C:L.185, C:F.188, C:F.195, C:Y.196, C:Y.196, C:I.205, C:A.208
- Hydrogen bonds: C:S.204
- Metal complexes: C:H.201
- 2 x BPB: BACTERIOPHEOPHYTIN B(Non-covalent)
BPB.9: 26 residues within 4Å:- Chain B: I.43, G.46, I.50, I.90, C.93, A.94, A.97, W.101, E.105, V.118, A.121, F.122, P.125, Y.149, G.150, I.151, H.154, A.238, F.242
- Chain C: Y.209, L.213, W.251, I.255
- Ligands: BCL.7, BCL.8, MQ7.15
14 PLIP interactions:13 interactions with chain B, 1 interactions with chain C- Hydrophobic interactions: B:I.43, B:I.50, B:I.90, B:A.97, B:A.121, B:F.122, B:F.122, B:F.122, B:P.125, B:Y.149, B:Y.149, B:F.242, B:F.242, C:Y.209
BPB.14: 21 residues within 4Å:- Chain B: F.182, M.186, L.190, F.217, V.220, V.221
- Chain C: F.60, S.64, I.67, S.124, L.125, W.128, V.132, I.145, N.148, F.149, S.272, M.276
- Ligands: BCL.6, BCL.13, NS5.16
12 PLIP interactions:3 interactions with chain B, 9 interactions with chain C- Hydrophobic interactions: B:F.182, B:M.186, B:L.190, C:F.60, C:I.67, C:I.67, C:W.128, C:I.145, C:N.148, C:F.149, C:F.149
- pi-Stacking: C:F.149
- 3 x MPG: [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate(Non-covalent)
MPG.10: 8 residues within 4Å:- Chain B: W.116, H.117, L.120, R.232, S.239
- Chain C: A.2, T.6, I.7
5 PLIP interactions:3 interactions with chain B, 2 interactions with chain C- Hydrophobic interactions: B:L.120, B:L.120, B:R.232, C:I.7
- Hydrogen bonds: C:A.2
MPG.11: 14 residues within 4Å:- Chain B: F.180, V.183, L.190, H.191, L.194, F.217, S.224, I.225, G.226, I.230, F.236, L.237
- Ligands: DGA.5, MPG.18
7 PLIP interactions:7 interactions with chain B- Hydrophobic interactions: B:F.180, B:V.183, B:F.236, B:L.237
- Hydrogen bonds: B:H.191, B:I.225, B:G.226
MPG.18: 4 residues within 4Å:- Chain C: G.31, G.48
- Ligands: BCL.6, MPG.11
No protein-ligand interaction detected (PLIP)- 1 x FE2: FE (II) ION(Non-covalent)
- 1 x MQ7: MENAQUINONE-7(Non-covalent)
MQ7.15: 23 residues within 4Å:- Chain B: Y.30, I.40, W.101, R.104
- Chain C: A.217, H.218, T.221, V.244, A.247, A.248, W.251, I.255, F.257, N.258, A.259, T.260, V.264, W.267, F.271
- Ligands: BCL.7, BCL.8, BPB.9, OTP.17
17 PLIP interactions:14 interactions with chain C, 3 interactions with chain B- Hydrophobic interactions: C:A.217, C:A.247, C:A.248, C:W.251, C:I.255, C:F.257, C:F.257, C:V.264, C:W.267, C:W.267, C:F.271, B:Y.30, B:Y.30, B:W.101
- Hydrogen bonds: C:H.218, C:A.259
- pi-Stacking: C:W.251
- 1 x NS5: 15-cis-1,2-dihydroneurosporene(Non-covalent)
- 1 x OTP: (2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)
OTP.17: 14 residues within 4Å:- Chain B: F.63, L.152
- Chain C: P.199, G.202, F.203, F.207, W.296, C.297, A.302
- Chain D: Q.14, W.25, L.29
- Ligands: BCL.8, MQ7.15
6 PLIP interactions:2 interactions with chain C, 1 interactions with chain B, 3 interactions with chain D- Hydrophobic interactions: C:F.207, C:A.302, B:F.63, D:Q.14, D:W.25, D:L.29
- 2 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.19: 7 residues within 4Å:- Chain C: W.24, Y.51, G.53, A.54, S.55, I.130, S.134
7 PLIP interactions:7 interactions with chain C- Hydrogen bonds: C:W.24, C:Y.51, C:A.54, C:S.55, C:S.55, C:S.134, C:S.134
PO4.20: 3 residues within 4Å:- Chain B: N.200
- Chain C: H.144, R.266
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:R.266
- Salt bridges: C:H.144
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Johansson, L.C. et al., Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography. Nat Commun (2013)
- Release Date
- 2013-12-25
- Peptides
- PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNIT: A
REACTION CENTER PROTEIN L CHAIN: B
REACTION CENTER PROTEIN M CHAIN: C
REACTION CENTER PROTEIN H CHAIN: D - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 3.50 Å
- Oligo State
- hetero-1-1-1-1-mer
- Ligands
- 4 x HEC: HEME C(Covalent)
- 1 x DGA: DIACYL GLYCEROL(Covalent)
- 4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)
- 2 x BPB: BACTERIOPHEOPHYTIN B(Non-covalent)
- 3 x MPG: [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate(Non-covalent)
- 1 x FE2: FE (II) ION(Non-covalent)
- 1 x MQ7: MENAQUINONE-7(Non-covalent)
- 1 x NS5: 15-cis-1,2-dihydroneurosporene(Non-covalent)
- 1 x OTP: (2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)
- 2 x PO4: PHOSPHATE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Johansson, L.C. et al., Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography. Nat Commun (2013)
- Release Date
- 2013-12-25
- Peptides
- PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNIT: A
REACTION CENTER PROTEIN L CHAIN: B
REACTION CENTER PROTEIN M CHAIN: C
REACTION CENTER PROTEIN H CHAIN: D - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D - Membrane
-
We predict this structure to be a membrane protein.