SMTL ID : 3dts.1

E(L212)A, D(L213)A, R(M233)L triple mutant structure of photosynthetic reaction center from Rhodobacter sphaeroides

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

hetero-1-1-1-mer

Ligands

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.1: 27 residues within 4Å: Chain A: F.97, A.124, I.125, A.127, Y.128, L.131, W.156, V.157, S.158, T.160, Y.162, N.166, F.167, H.168, H.173, A.176, I.177, F.180, S.244, A.245, C.247, M.248 Chain B: Y.210 Ligands: BCL.2, BPH.5, BCL.6, BCL.8 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:F.97, A:F.97, A:A.124, A:A.127, A:T.160, A:Y.162, A:F.167, A:A.176, A:I.177, A:I.177, A:I.177, A:F.180, B:Y.210 Hydrogen bonds: A:S.244 Metal complexes: A:H.173 BCL.2: 19 residues within 4Å: Chain A: Y.128, L.131, F.146, I.150, H.153, L.154, V.157 Chain B: F.197, G.203, I.206, A.207, Y.210, G.211, L.214 Ligands: BCL.1, BPH.5, BCL.8, U10.10, LDA.13 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B, Hydrophobic interactions: A:Y.128, A:L.131, A:L.154, A:V.157, B:F.197, B:I.206, B:L.214 Metal complexes: A:H.153 pi-Stacking: B:Y.210 BCL.6: 19 residues within 4Å: Chain A: H.168, M.174, I.177, S.178, F.181, T.182 Chain B: W.66, W.157, L.160, I.179, H.182, L.183, W.185, T.186 Ligands: BCL.1, U10.3, BPH.7, BCL.8, SPN.11 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A, Hydrophobic interactions: B:W.66, B:L.160, B:I.179, B:L.183, B:W.185, B:T.186, A:I.177, A:I.177 Metal complexes: B:H.182 BCL.8: 28 residues within 4Å: Chain A: V.157, Y.162, F.181 Chain B: W.66, M.122, V.126, A.153, L.156, W.157, L.160, T.186, N.187, F.189, S.190, L.196, F.197, H.202, S.205, I.206, L.209, Y.210, V.276, G.280, I.284 Ligands: BCL.1, BCL.2, BCL.6, BPH.7 18 PLIP interactions: 17 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:W.66, B:V.126, B:L.156, B:W.157, B:T.186, B:N.187, B:F.189, B:F.197, B:F.197, B:F.197, B:I.206, B:I.206, B:L.209, B:Y.210, B:V.276, B:I.284, A:V.157 Metal complexes: B:H.202

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

U10.3: 15 residues within 4Å: Chain A: I.175, S.178, F.179, L.189, H.190, L.193, A.213, F.216, Y.222, S.223, I.224, G.225, I.229, L.232 Ligands: BCL.6 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.175, A:F.179, A:L.189, A:F.216, A:F.216, A:F.216, A:Y.222 Hydrogen bonds: A:I.224, A:G.225 U10.10: 20 residues within 4Å: Chain A: G.35, W.100 Chain B: M.218, H.219, T.222, A.248, A.249, W.252, M.256, F.258, N.259, A.260, M.262, I.265, W.268, M.272 Ligands: BCL.2, BPH.5, LDA.14, LDA.15 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:M.218, B:W.252, B:M.256, B:F.258, B:F.258, B:A.260, B:I.265, B:W.268, B:W.268, A:W.100, A:W.100, A:W.100 Hydrogen bonds: B:T.222, B:A.260

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

LDA.4: 7 residues within 4Å: Chain A: L.75, G.76, G.77, T.90, I.91, T.94, W.142 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.90, A:I.91, A:T.94, A:W.142, A:W.142 LDA.13: 9 residues within 4Å: Chain B: P.200, L.204, A.207, F.208, W.268, M.272 Chain C: W.21 Ligands: BCL.2, LDA.15 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.204, B:A.207, B:F.208, B:W.268 LDA.14: 4 residues within 4Å: Chain A: P.28 Chain B: M.256, F.258 Ligands: U10.10 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.28, B:F.258 LDA.15: 7 residues within 4Å: Chain B: G.257, F.258 Chain C: Q.32, Y.40, Q.53 Ligands: U10.10, LDA.13 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.258, B:F.258, B:F.258

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.5: 25 residues within 4Å: Chain A: F.41, A.93, A.96, F.97, W.100, E.104, I.117, A.120, F.121, A.124, Y.128, G.149, I.150, H.153, L.238, V.241 Chain B: Y.210, A.213, L.214, M.218, W.252, M.256 Ligands: BCL.1, BCL.2, U10.10 10 PLIP interactions: 2 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:A.213, B:L.214, A:A.96, A:A.120, A:F.121, A:A.124, A:L.238, A:V.241, A:V.241 pi-Stacking: A:F.121 BPH.7: 21 residues within 4Å: Chain A: F.181, A.184, L.185, A.188, L.189, V.220 Chain B: S.59, G.63, F.67, A.125, V.126, W.129, T.146, A.149, F.150, S.152, A.153, A.273, T.277 Ligands: BCL.6, BCL.8 13 PLIP interactions: 3 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:A.184, A:A.188, A:L.189, B:F.67, B:F.67, B:F.67, B:A.125, B:A.149, B:F.150, B:F.150, B:A.153, B:T.277 pi-Stacking: B:F.150

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

FE.9: 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

1 x SPN: SPEROIDENONE(Non-covalent)

SPN.11: 20 residues within 4Å: Chain B: W.66, F.67, I.70, G.71, F.74, W.75, F.85, W.115, S.119, M.122, W.157, L.160, G.161, F.162, V.175, Y.177, G.178, I.179, H.182 Ligands: BCL.6 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:W.66, B:F.67, B:F.67, B:F.67, B:I.70, B:I.70, B:F.74, B:F.74, B:F.85, B:W.115, B:W.157, B:L.160, B:F.162, B:F.162, B:F.162, B:V.175, B:V.175, B:Y.177, B:I.179

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.12: 16 residues within 4Å: Chain A: N.199, P.200 Chain B: G.143, K.144, H.145, W.148, S.152, W.155, R.267, I.270, W.271, L.278, I.282 Chain C: I.22, G.26, Y.30 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:W.148, B:W.148, B:W.155, B:W.155, B:I.270, B:W.271, B:L.278, B:I.282, C:Y.30, C:Y.30 Hydrogen bonds: B:K.144 Salt bridges: B:K.144, B:H.145, B:H.145, B:H.145, B:R.267, B:R.267

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pokkuluri, P.R. et al., Structural description of compensatory mutations that restore proton transfer pathways to the L212-L213A mutant bacterial reaction center. To be Published

Release Date

2009-06-30

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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