SMTL ID : 1yf6.1

Structure of a quintuple mutant of photosynthetic reaction center from rhodobacter sphaeroides

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

hetero-1-1-1-mer

Ligands

5 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.1: 27 residues within 4Å: Chain A: F.97, A.124, I.125, A.127, L.131, W.156, V.157, T.160, G.161, Y.162, N.166, F.167, H.168, H.173, A.176, I.177, F.180, Y.181, S.244, A.245, C.247, M.248 Chain B: F.210 Ligands: BCL.2, BCL.14, BCL.15, BCL.16 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain B, Hydrophobic interactions: A:F.97, A:F.97, A:F.97, A:A.127, A:T.160, A:Y.162, A:F.167, A:A.176, A:I.177, A:F.180, A:F.180, B:F.210, B:F.210 Hydrogen bonds: A:S.244 Metal complexes: A:H.173 BCL.2: 20 residues within 4Å: Chain A: I.49, Y.128, L.131, F.146, I.150, H.153, L.154, V.157 Chain B: F.197, D.203, I.206, A.207, F.210, G.211, H.214 Ligands: BCL.1, LDA.7, BCL.15, BCL.16, U10.17 11 PLIP interactions: 6 interactions with chain A, 5 interactions with chain B, Hydrophobic interactions: A:I.49, A:L.131, A:F.146, A:L.154, A:V.157, B:F.197, B:I.206, B:I.206, B:F.210 Metal complexes: A:H.153 pi-Stacking: B:F.210 BCL.14: 17 residues within 4Å: Chain A: H.168, M.174, I.177, S.178, Y.181, T.182, L.185 Chain B: M.122, W.157, I.179, H.182, L.183, T.186 Ligands: BCL.1, BPH.3, BCL.15, SPO.18 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A, Hydrophobic interactions: B:I.179, B:L.183, A:I.177, A:I.177, A:L.185 Metal complexes: B:H.182 Hydrogen bonds: A:T.182 Water bridges: A:H.173 pi-Stacking: A:Y.181 BCL.15: 28 residues within 4Å: Chain A: V.157, Y.162, H.168, Y.181 Chain B: M.122, A.153, L.156, W.157, L.160, T.186, N.187, F.189, S.190, N.195, L.196, F.197, H.202, S.205, I.206, L.209, F.210, V.276, G.280, I.284 Ligands: BCL.1, BCL.2, BPH.3, BCL.14 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:L.156, B:T.186, B:F.189, B:L.196, B:F.197, B:F.197, B:I.206, B:I.206, B:I.206, B:L.209, B:F.210, B:V.276 Metal complexes: B:H.202 BCL.16: 31 residues within 4Å: Chain A: T.38, I.49, A.93, A.96, F.97, W.100, E.104, I.117, A.120, F.121, F.123, A.124, Y.128, Y.148, G.149, I.150, H.153, S.237, L.238, V.241 Chain B: F.210, A.213, H.214, A.217, M.218, W.252, T.255, M.256, F.258 Ligands: BCL.1, BCL.2 15 PLIP interactions: 12 interactions with chain A, 3 interactions with chain B, Hydrophobic interactions: A:I.49, A:A.93, A:A.120, A:F.121, A:F.121, A:F.121, A:F.123, A:A.124, A:Y.148, A:L.238, A:V.241, A:V.241, B:A.213 Salt bridges: B:H.214 Metal complexes: B:H.214

1 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.3: 22 residues within 4Å: Chain A: Y.181, A.184, L.185, L.189, F.216, L.219, V.220 Chain B: S.59, L.60, G.63, A.125, V.126, W.129, T.133, T.146, A.149, F.150, A.153, A.273, T.277 Ligands: BCL.14, BCL.15 11 PLIP interactions: 3 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:A.184, A:L.185, A:L.189, B:L.60, B:W.129, B:A.149, B:F.150, B:F.150, B:F.150, B:A.153, B:T.277

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

U10.4: 11 residues within 4Å: Chain A: A.186, L.189, H.190, L.193, F.216, Y.222, S.223, I.224, G.225, I.229, L.232 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.232 Hydrogen bonds: A:I.224 Water bridges: A:G.225 pi-Stacking: A:F.216 U10.5: 6 residues within 4Å: Chain A: W.263, W.265, W.266 Chain B: L.86, L.89, F.90 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.89, B:F.90, A:W.266 pi-Stacking: A:W.266, A:W.266 U10.17: 6 residues within 4Å: Chain B: F.258, N.259, W.260, W.268 Chain C: Q.32 Ligands: BCL.2 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:Q.32 pi-Stacking: B:F.258, B:W.268

1 x HTO: HEPTANE-1,2,3-TRIOL(Non-covalent)

HTO.6: 4 residues within 4Å: Chain A: A.101, Y.115, P.118, F.119 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.101

3 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)

LDA.7: 10 residues within 4Å: Chain A: W.151 Chain B: P.200, D.203, L.204, F.208, W.268, M.272 Chain C: W.21, L.31 Ligands: BCL.2 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:L.31, B:F.208, B:W.268 Hydrogen bonds: B:P.200 LDA.8: 7 residues within 4Å: Chain A: L.75, G.76, G.77, Q.87, I.91, L.133, W.142 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Q.87, A:I.91, A:L.133, A:W.142, A:W.142 LDA.20: 6 residues within 4Å: Chain B: F.105, A.106, A.107, P.108, L.109, I.117 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.117

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 6 residues within 4Å: Chain A: R.7 Chain C: E.43, E.45, D.46, G.47, I.85 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Water bridges: C:E.43 Hydrogen bonds: A:R.7

1 x FE2: FE (II) ION(Non-covalent)

FE2.10: 5 residues within 4Å: Chain A: H.190, H.230 Chain B: H.219, E.234, H.266 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Metal complexes: A:H.190, A:H.230, B:H.219, B:E.234, B:H.266

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.11: 4 residues within 4Å: Chain B: H.219, T.222, W.260, I.265 Ligand excluded by PLIP

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.12: 4 residues within 4Å: Chain B: N.25, N.28, G.53, S.54 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.25, B:N.28, B:S.54, B:S.54, B:S.54 Water bridges: B:Y.51 PO4.13: 2 residues within 4Å: Chain B: T.21 Chain C: H.126 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:T.21 Water bridges: B:T.21, B:T.21 Salt bridges: C:H.126

1 x SPO: SPHEROIDENE(Non-covalent)

SPO.18: 22 residues within 4Å: Chain B: F.67, I.70, G.71, F.74, W.75, F.85, L.89, 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: BCL.14 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:F.67, B:F.67, B:F.67, B:I.70, B:F.74, B:F.85, B:L.89, B:W.115, B:W.157, B:L.160, B:W.171, B:V.175, B:V.175, B:Y.177, B:I.179

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.19: 16 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, Y.30 20 PLIP interactions: 14 interactions with chain B, 4 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: B:W.148, B:W.148, B:W.155, B:W.155, B:I.270, B:W.271, B:L.278, C:F.20, C:I.22, C:F.23, C:F.23 Hydrogen bonds: B:K.144 Water bridges: B:K.144, B:R.267, A:N.199, A:K.202 Salt bridges: B:H.145, B:H.145, B:H.145, B:R.267

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Paddock, M.L. et al., Quinone (Q(B)) Reduction by B-Branch Electron Transfer in Mutant Bacterial Reaction Centers from Rhodobacter sphaeroides: Quantum Efficiency and X-ray Structure. Biochemistry (2005)

Release Date

2005-05-17

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
L

B
M

C
H

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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