SMTL ID : 5lri.1

PHOTOSYNTHETIC REACTION CENTER MUTANT WITH GLUL212 REPLACED WITH TRP (CHAIN L, EL212W)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 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, T.160, G.161, Y.162, N.166, F.167, H.168, H.173, A.176, I.177, F.180, S.244, C.247, M.248 Chain B: Y.210 Ligands: BPH.2, BCL.9, BCL.10, BCL.11, U10.13 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: 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:F.180, A:F.180, B:Y.210 Hydrogen bonds: A:S.244 Metal complexes: A:H.173 BCL.9: 19 residues within 4Å: Chain A: H.168, M.174, I.177, S.178, F.181, T.182 Chain B: W.66, M.122, W.157, L.160, V.175, I.179, H.182, L.183, T.186 Ligands: BCL.1, BCL.10, BPH.12, SPN.14 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A, Hydrophobic interactions: B:W.66, 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.10: 27 residues within 4Å: Chain A: V.157, Y.162, F.181 Chain B: W.66, M.122, 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.9, BCL.11, BPH.12 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:W.66, 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:Y.210, B:V.276, B:I.284 Metal complexes: B:H.202 BCL.11: 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.2, LDA.6, BCL.10, U10.13 12 PLIP interactions: 6 interactions with chain A, 6 interactions with chain B, Hydrophobic interactions: 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

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.2: 31 residues within 4Å: Chain A: T.38, A.42, I.49, C.92, 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, M.218, W.252, T.255, M.256 Ligands: BCL.1, BCL.11, U10.13 19 PLIP interactions: 16 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.49, A:A.96, A:A.120, A:F.121, A:F.121, A:F.121, A:F.123, A:Y.128, A:Y.148, A:Y.148, A:Y.148, A:I.150, A:L.238, A:V.241, A:V.241, B:Y.210, B:A.213, B:L.214 Hydrogen bonds: A:E.104 BPH.12: 24 residues within 4Å: Chain A: F.181, A.184, L.185, A.188, L.189, F.216, L.219 Chain B: S.59, G.63, W.66, F.67, A.125, V.126, W.129, T.133, T.146, A.149, F.150, A.153, A.273, V.274, T.277 Ligands: BCL.9, BCL.10 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.66, B:F.67, B:A.125, B:W.129, B:W.129, B:A.149, B:F.150, B:F.150, B:T.277, A:F.181, A:A.184, A:L.189 pi-Stacking: B:F.150

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

U10.3: 18 residues within 4Å: Chain A: I.175, S.178, T.182, L.189, H.190, L.193, W.212, D.213, F.216, V.220, Y.222, S.223, I.224, G.225, T.226, I.229, W.263 Chain B: F.90 13 PLIP interactions: 1 interactions with chain B, 12 interactions with chain A Hydrophobic interactions: B:F.90, A:I.175, A:T.182, A:L.189, A:L.193, A:F.216, A:F.216, A:V.220, A:I.224, A:W.263 Hydrogen bonds: A:D.213, A:I.224, A:G.225 U10.13: 27 residues within 4Å: Chain A: F.29, Y.30, G.35, T.38, W.100, R.103 Chain B: 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, BPH.2, LDA.7, LDA.8, BCL.11 16 PLIP interactions: 10 interactions with chain B, 6 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:F.29, A:F.29, A:T.38, A:W.100, A:W.100, A:W.100 Hydrogen bonds: B:A.260

3 x DD9: nonane(Non-covalent)

DD9.4: 3 residues within 4Å: Chain A: P.61, Y.148 Ligands: LDA.17 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.61 DD9.18: 3 residues within 4Å: Chain C: W.21 Ligands: LDA.6, LDA.17 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.21 DD9.19: 1 residues within 4Å: Chain C: A.25 No protein-ligand interaction detected (PLIP)

1 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: 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

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

LDA.6: 9 residues within 4Å: Chain A: W.151 Chain B: P.200, A.207, F.208, W.268, M.272 Ligands: LDA.7, BCL.11, DD9.18 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.207, B:F.208, B:W.268 LDA.7: 10 residues within 4Å: Chain B: G.257, F.258 Chain C: Q.32, Y.40, L.42, Q.53, F.56 Ligands: LDA.6, LDA.8, U10.13 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:Y.40 Water bridges: C:Y.40 Hydrophobic interactions: B:F.258 LDA.8: 7 residues within 4Å: Chain A: P.28, F.29 Chain B: M.256, G.257 Ligands: LDA.7, U10.13, LDA.17 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.29 LDA.16: 5 residues within 4Å: Chain B: F.7, L.38, L.39, W.41, F.42 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.7, B:L.38, B:L.39, B:W.41, B:F.42 pi-Cation interactions: B:W.41, B:W.41 LDA.17: 4 residues within 4Å: Chain C: W.21 Ligands: DD9.4, LDA.8, DD9.18 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:W.21 Hydrogen bonds: C:W.21 pi-Cation interactions: C:W.21, C:W.21

1 x SPN: SPEROIDENONE(Non-covalent)

SPN.14: 22 residues within 4Å: Chain B: W.66, F.67, F.68, I.70, G.71, F.74, W.75, W.115, S.119, 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.9 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:W.66, B:F.67, B:F.67, B:F.67, B:F.68, B:I.70, B:I.70, B:F.74, B:F.74, 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:I.179

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.15: 19 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, V.274, L.278 Chain C: A.16, I.22, F.23, G.26, L.27, Y.30 25 PLIP interactions: 18 interactions with chain B, 7 interactions with chain C Hydrophobic interactions: B:W.148, B:W.148, B:W.155, B:W.155, B:W.155, B:I.270, B:W.271, B:W.271, B:V.274, B:L.278, B:L.278, C:I.22, C:F.23, C:F.23, C:F.23, C:Y.30, C:Y.30 Hydrogen bonds: B:K.144 Water bridges: B:K.144, B:R.267, 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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