SMTL ID : 5lse.1

PHOTOSYNTHETIC REACTION CENTER MUTANT WITH Glu L212 replaced with Ala (CHAIN L, EL212W), Asp L213 replaced with ALA (Chain L, DL213A) AND LEU M215 REPLACED WITH ALA (CHAIN M, LM215A)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-oligomer

Ligands

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.1: 29 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, G.161, 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.3, BCL.7, BCL.8, U10.10 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:F.97, A:F.97, A:A.124, A:A.127, A:V.157, A:T.160, A:Y.162, A:F.167, A:A.176, A:I.177, A:I.177, A:F.180, A:F.180, B:Y.210 Hydrogen bonds: A:S.244 Metal complexes: A:H.173 BCL.2: 20 residues within 4Å: Chain A: I.46, 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.3, BCL.8, U10.10, LDA.12 13 PLIP interactions: 7 interactions with chain A, 6 interactions with chain B, Hydrophobic interactions: A:I.46, A:Y.128, A:L.131, A:F.146, A:L.154, A:V.157, B:F.197, B:I.206, B:I.206, B:Y.210, B:L.214 Metal complexes: A:H.153 pi-Stacking: B:Y.210 BCL.7: 20 residues within 4Å: Chain A: H.168, M.174, I.177, S.178, F.181, T.182 Chain B: W.66, F.67, M.122, W.157, L.160, V.175, I.179, H.182, L.183, T.186 Ligands: BCL.1, BCL.8, BPH.9, SPN.11 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A, Hydrophobic interactions: B:W.66, B:F.67, B:L.160, B:V.175, B:L.183, A:I.177, A:I.177 Metal complexes: B:H.182 pi-Stacking: A:F.181 BCL.8: 28 residues within 4Å: Chain A: V.157, Y.162, H.168, F.181 Chain B: V.126, 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, Y.210, V.276, G.280, I.284 Ligands: BCL.1, BCL.2, BCL.7, BPH.9 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:V.126, B:V.126, B:A.153, B:L.156, B:W.157, B:T.186, B:F.189, B:L.196, B:I.206, B:L.209, B:L.209, B:Y.210, B:V.276 Metal complexes: B:H.202

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.3: 32 residues within 4Å: Chain A: T.38, F.41, A.42, 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, L.238, V.241 Chain B: Y.210, A.213, L.214, A.217, M.218, W.252, T.255, M.256 Ligands: BCL.1, BCL.2, U10.10 21 PLIP interactions: 17 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:A.42, A:I.49, A:A.93, A:A.96, A:A.120, A:F.121, A:F.121, A:F.121, A:F.123, A:A.124, A:Y.128, A:Y.148, A:Y.148, A:L.238, A:V.241, A:V.241, B:Y.210, B:A.213, B:L.214, B:A.217 Hydrogen bonds: A:E.104 BPH.9: 24 residues within 4Å: Chain A: F.181, A.184, L.185, L.189, L.219, V.220 Chain B: S.59, L.60, G.63, L.64, W.66, F.67, A.125, V.126, W.129, T.133, T.146, A.149, F.150, A.153, A.273, T.277 Ligands: BCL.7, BCL.8 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.60, B:W.66, B:F.67, B:W.129, B:A.149, B:F.150, B:F.150, B:A.153, B:T.277, A:F.181, A:A.184, A:L.189 pi-Stacking: B:F.150

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

U10.4: 17 residues within 4Å: Chain A: M.174, S.178, F.179, T.182, L.189, H.190, L.193, V.194, F.216, Y.222, S.223, I.224, G.225, T.226, I.229, W.263 Chain B: F.90 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.179, A:T.182, A:L.189, A:L.193, A:F.216, A:Y.222, A:I.224, A:I.229, A:I.229, B:F.90 Hydrogen bonds: A:I.224, A:G.225 U10.10: 25 residues within 4Å: Chain A: F.29, G.35, W.100, R.103 Chain B: L.214, M.218, H.219, T.222, I.223, A.248, A.249, W.252, M.256, F.258, N.259, A.260, T.261, M.262, I.265, W.268, M.272 Ligands: BCL.1, BCL.2, BPH.3, LDA.16 16 PLIP interactions: 13 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.214, B:M.218, B:H.219, B:W.252, B:M.256, B:F.258, B:F.258, B:A.260, B:I.265, B:I.265, B:W.268, B:W.268, A:F.29, A:W.100, A:W.100 Hydrogen bonds: B:A.260

5 x D12: DODECANE(Non-covalent)

D12.5: 3 residues within 4Å: Chain A: Q.62 Ligands: LDA.12, D12.19 No protein-ligand interaction detected (PLIP) D12.17: 5 residues within 4Å: Chain C: A.25, Y.29 Ligands: CDL.15, D12.18, D12.20 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.29, C:Y.29 D12.18: 5 residues within 4Å: Chain C: W.21, A.25, I.28 Ligands: D12.17, D12.19 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:W.21, C:W.21, C:A.25, C:I.28 D12.19: 3 residues within 4Å: Chain C: W.21 Ligands: D12.5, D12.18 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.21 D12.20: 2 residues within 4Å: Chain C: P.55 Ligands: D12.17 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:P.55

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

FE.6: 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: 23 residues within 4Å: Chain B: F.67, F.68, I.70, G.71, F.74, W.75, F.85, W.115, S.119, F.120, M.122, W.157, M.158, L.160, G.161, F.162, W.171, V.175, Y.177, G.178, I.179, H.182 Ligands: BCL.7 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:F.67, B:F.67, B:F.67, B:I.70, B:I.70, B:F.74, B:F.85, B:W.115, B:W.157, B:L.160, B:F.162, B:W.171, B:V.175, B:V.175, B:Y.177, B:Y.177, B:I.179

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

LDA.12: 9 residues within 4Å: Chain B: P.200, G.203, L.204, A.207, F.208 Chain C: W.21 Ligands: BCL.2, D12.5, LDA.16 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.207, B:F.208 LDA.13: 5 residues within 4Å: Chain A: P.28, F.29 Chain B: M.256, G.257 Ligands: LDA.16 No protein-ligand interaction detected (PLIP) LDA.16: 9 residues within 4Å: Chain B: F.258 Chain C: I.28, Q.32, Y.40, Q.53, F.56 Ligands: U10.10, LDA.12, LDA.13 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:I.28, C:F.56, B:F.258, B:F.258

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

PO4.14: 3 residues within 4Å: Chain B: N.28, G.53, S.54 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.28, B:N.28, B:S.54, B:S.54 Water bridges: B:L.55

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.15: 17 residues within 4Å: Chain A: N.199, P.200 Chain B: G.143, K.144, H.145, W.148, W.155, R.267, W.271, V.274, L.278 Chain C: A.16, I.22, F.23, G.26, Y.30 Ligands: D12.17 20 PLIP interactions: 14 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:W.148, B:W.155, B:W.155, B:W.271, B:W.271, B:V.274, B:L.278, C:I.22, C:F.23, C:F.23, C:F.23, C:Y.30 Hydrogen bonds: B:K.144, B:R.267 Water bridges: B:K.144, C:Y.30 Salt bridges: B:H.145, B:H.145, B:H.145, B:R.267

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Friebe, V.M. et al., On the mechanism of ubiquinone mediated photocurrent generation by a reaction center based photocathode. Biochim.Biophys.Acta (2016)

Release Date

2016-11-09

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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