SMTL ID : 1z9k.2 (1 other biounit)

Photosynthetic Reaction Center from Rhodobacter sphaeroides

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 4.60 Å

Oligo State

hetero-2-2-2-mer

Ligands

8 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.1: 13 residues within 4Å: Chain A: M.174, I.177, S.178, F.181, T.182 Chain B: M.122, H.182, L.183, T.186 Ligands: BCL.2, U10.4, BCL.6, BPH.8 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A, pi-Stacking: B:H.182, B:H.182, A:F.181, A:F.181 Metal complexes: B:H.182 Hydrophobic interactions: A:I.177, A:F.181, A:T.182 BCL.2: 22 residues within 4Å: Chain A: F.97, A.124, A.127, Y.128, L.131, V.157, S.158, Y.162, N.166, F.167, H.168, H.173, I.177, F.180, S.244, A.245, C.247, M.248 Ligands: BCL.1, BPH.3, BCL.6, BCL.7 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:F.97, A:F.97, A:A.127, A:V.157, A:Y.162, A:F.167, A:F.167, A:I.177, A:F.180, A:F.180 pi-Stacking: A:H.173, A:H.173 Metal complexes: A:H.173 BCL.6: 23 residues within 4Å: Chain A: Y.162, F.181 Chain B: A.153, L.156, W.157, L.160, T.186, N.187, F.189, S.190, F.197, F.201, H.202, S.205, I.206, L.209, Y.210, G.280, I.284 Ligands: BCL.1, BCL.2, BCL.7, BPH.8 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:A.153, B:W.157, B:T.186, B:F.189, B:F.197, B:F.197, B:I.206, B:L.209, B:Y.210 pi-Stacking: B:H.202, B:H.202 pi-Cation interactions: B:H.202 Metal complexes: B:H.202 BCL.7: 14 residues within 4Å: Chain A: Y.128, F.146, H.153, L.154 Chain B: F.197, H.202, G.203, I.206, A.207, Y.210, G.211 Ligands: BCL.2, BPH.3, BCL.6 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A, Hydrophobic interactions: B:F.197, B:I.206, B:A.207, A:Y.128, A:F.146, A:L.154 pi-Stacking: A:H.153, A:H.153 BCL.11: 13 residues within 4Å: Chain D: M.174, I.177, S.178, F.181, T.182 Chain E: M.122, H.182, L.183, T.186 Ligands: BCL.12, U10.14, BCL.16, BPH.18 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain E, Hydrophobic interactions: D:I.177, D:F.181, D:T.182 pi-Stacking: D:F.181, D:F.181, E:H.182, E:H.182 Metal complexes: E:H.182 BCL.12: 22 residues within 4Å: Chain D: F.97, A.124, A.127, Y.128, L.131, V.157, S.158, Y.162, N.166, F.167, H.168, H.173, I.177, F.180, S.244, A.245, C.247, M.248 Ligands: BCL.11, BPH.13, BCL.16, BCL.17 13 PLIP interactions: 13 interactions with chain D, Hydrophobic interactions: D:F.97, D:F.97, D:A.127, D:V.157, D:Y.162, D:F.167, D:F.167, D:I.177, D:F.180, D:F.180 pi-Stacking: D:H.173, D:H.173 Metal complexes: D:H.173 BCL.16: 23 residues within 4Å: Chain D: Y.162, F.181 Chain E: A.153, L.156, W.157, L.160, T.186, N.187, F.189, S.190, F.197, F.201, H.202, S.205, I.206, L.209, Y.210, G.280, I.284 Ligands: BCL.11, BCL.12, BCL.17, BPH.18 13 PLIP interactions: 13 interactions with chain E, Hydrophobic interactions: E:A.153, E:W.157, E:T.186, E:F.189, E:F.197, E:F.197, E:I.206, E:L.209, E:Y.210 pi-Stacking: E:H.202, E:H.202 pi-Cation interactions: E:H.202 Metal complexes: E:H.202 BCL.17: 14 residues within 4Å: Chain D: Y.128, F.146, H.153, L.154 Chain E: F.197, H.202, G.203, I.206, A.207, Y.210, G.211 Ligands: BCL.12, BPH.13, BCL.16 8 PLIP interactions: 3 interactions with chain E, 5 interactions with chain D, Hydrophobic interactions: E:F.197, E:I.206, E:A.207, D:Y.128, D:F.146, D:L.154 pi-Stacking: D:H.153, D:H.153

4 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.3: 26 residues within 4Å: Chain A: A.42, I.46, A.93, F.97, W.100, E.104, I.117, A.120, F.121, A.124, Y.148, G.149, I.150, H.153, L.238, V.241 Chain B: Y.210, A.213, L.214, A.217, M.218, W.252, M.256 Ligands: BCL.2, BCL.7, U10.9 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:A.42, A:I.46, A:A.93, A:A.120, A:A.124, A:Y.148, A:I.150, A:L.238, A:V.241, B:Y.210, B:A.213 pi-Stacking: A:F.121 BPH.8: 21 residues within 4Å: Chain A: F.181, T.182, A.184, L.185, A.188, L.189, L.219 Chain B: L.60, G.63, L.64, A.125, V.126, W.129, A.149, F.150, A.273, V.274, T.277 Ligands: BCL.1, U10.4, BCL.6 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.60, B:L.64, B:F.150, B:F.150, B:T.277, A:F.181, A:A.184, A:L.189 pi-Stacking: B:F.150 BPH.13: 26 residues within 4Å: Chain D: A.42, I.46, A.93, F.97, W.100, E.104, I.117, A.120, F.121, A.124, Y.148, G.149, I.150, H.153, L.238, V.241 Chain E: Y.210, A.213, L.214, A.217, M.218, W.252, M.256 Ligands: BCL.12, BCL.17, U10.19 12 PLIP interactions: 2 interactions with chain E, 10 interactions with chain D Hydrophobic interactions: E:Y.210, E:A.213, D:A.42, D:I.46, D:A.93, D:A.120, D:A.124, D:Y.148, D:I.150, D:L.238, D:V.241 pi-Stacking: D:F.121 BPH.18: 21 residues within 4Å: Chain D: F.181, T.182, A.184, L.185, A.188, L.189, L.219 Chain E: L.60, G.63, L.64, A.125, V.126, W.129, A.149, F.150, A.273, V.274, T.277 Ligands: BCL.11, U10.14, BCL.16 9 PLIP interactions: 6 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:L.60, E:L.64, E:F.150, E:F.150, E:T.277, D:F.181, D:A.184, D:L.189 pi-Stacking: E:F.150

4 x U10: UBIQUINONE-10(Non-covalent)

U10.4: 11 residues within 4Å: Chain A: L.193, F.216, V.220, Y.222, S.223, I.224, G.225, I.229, L.232 Ligands: BCL.1, BPH.8 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.220 U10.9: 15 residues within 4Å: Chain A: T.38 Chain B: L.215, M.218, H.219, T.222, A.248, A.249, W.252, M.256, N.259, A.260, T.261, I.265, W.268 Ligands: BPH.3 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.215, B:M.218, B:W.252, B:A.260, B:I.265, B:W.268 Hydrogen bonds: B:A.260 U10.14: 11 residues within 4Å: Chain D: L.193, F.216, V.220, Y.222, S.223, I.224, G.225, I.229, L.232 Ligands: BCL.11, BPH.18 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:V.220 U10.19: 15 residues within 4Å: Chain D: T.38 Chain E: L.215, M.218, H.219, T.222, A.248, A.249, W.252, M.256, N.259, A.260, T.261, I.265, W.268 Ligands: BPH.13 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:L.215, E:M.218, E:W.252, E:A.260, E:I.265, E:W.268 Hydrogen bonds: E:H.219, E:T.222, E:A.260

2 x FE: FE (III) ION(Non-covalent)

FE.5: 5 residues within 4Å: Chain A: H.190, H.230 Chain B: H.219, E.234, H.266 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Metal complexes: B:H.219, B:E.234, B:H.266, A:H.190, A:H.230 FE.15: 5 residues within 4Å: Chain D: H.190, H.230 Chain E: H.219, E.234, H.266 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain E Metal complexes: D:H.190, D:H.230, E:H.219, E:E.234, E:H.266

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.10: 3 residues within 4Å: Chain C: H.128 Chain F: H.128 Ligands: MN.20 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain C Metal complexes: F:H.128, C:H.128 MN.20: 3 residues within 4Å: Chain C: H.128 Chain F: H.128 Ligands: MN.10 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain F Metal complexes: C:H.128, F:H.128

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Uyeda, G. et al., Design of a Redox-Linked Active Metal Site: Manganese Bound to Bacterial Reaction Centers at a Site Resembling That of Photosystem II. Biochemistry (2005)

Release Date

2005-06-07

Peptides

Reaction center protein L chain: AD
Reaction center protein M chain: BE
Reaction center protein H chain: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

B
B

E
B

C
C

F
C

Membrane

We predict this structure to be a membrane protein.
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Reaction center protein L chain

Reaction center protein M chain

Reaction center protein H chain

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