SMTL ID : 4lwy.1

L(M196)H,H(M202)L Double Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

LDA.1: 9 residues within 4Å: Chain A: I.28, Q.32, Y.40, Q.53, F.56 Chain C: G.258, F.259 Ligands: U10.31, LDA.33 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:I.28, C:F.259, C:F.259 Hydrogen bonds: A:Y.40 Water bridges: C:R.254 LDA.33: 11 residues within 4Å: Chain A: W.21 Chain C: P.201, G.204, L.205, F.209, W.269, M.273 Ligands: LDA.1, UNL.4, UNL.5, BCL.28 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:W.21, A:W.21, C:L.205, C:F.209, C:W.269 LDA.34: 6 residues within 4Å: Chain C: F.8, L.39, L.40, W.42, F.43 Ligands: U10.17 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.8, C:L.40, C:W.42, C:W.42, C:F.43 pi-Cation interactions: C:W.42 LDA.35: 9 residues within 4Å: Chain B: V.221, G.222, Y.223 Chain C: S.31, G.32, V.33, G.34, G.49 Ligands: UNL.39 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.223 LDA.36: 7 residues within 4Å: Chain C: F.106, A.107, A.108, P.109, L.110, I.118, F.121 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.106, C:I.118, C:F.121, C:F.121 Hydrogen bonds: C:A.107 LDA.37: 6 residues within 4Å: Chain C: R.14, V.33, G.34, P.35, F.36, T.38 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.36 Hydrogen bonds: C:R.14, C:T.38, C:T.38

11 x UNL: UNKNOWN LIGAND

UNL.2: 5 residues within 4Å: Chain A: A.25, Y.29 Ligands: UNL.3, UNL.4, CDL.26 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.29, A:Y.29 UNL.3: 4 residues within 4Å: Chain A: Y.29, P.55, F.56 Ligands: UNL.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.29, A:P.55 UNL.4: 6 residues within 4Å: Chain A: Y.18, W.21 Ligands: UNL.2, UNL.5, LDA.33, UNL.38 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.18, A:W.21 UNL.5: 4 residues within 4Å: Chain A: Y.18, W.21 Ligands: UNL.4, LDA.33 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.18, A:W.21, A:W.21, A:W.21, A:W.21 UNL.18: 8 residues within 4Å: Chain B: G.77, G.78, Q.88, T.91, I.92, T.95, L.134, W.143 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Q.88, B:T.91, B:I.92, B:L.134, B:W.143, B:W.143 UNL.19: 5 residues within 4Å: Chain B: A.102, R.110, Y.116, P.119 Ligands: UNL.21 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.102, B:Y.116 UNL.20: 2 residues within 4Å: Chain B: F.135, F.243 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.135, B:F.243 UNL.21: 4 residues within 4Å: Chain B: Y.116, F.120 Chain C: Q.5 Ligands: UNL.19 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:Y.116, B:Y.116, B:F.120, C:Q.5 UNL.38: 6 residues within 4Å: Chain B: F.30 Chain C: M.257, G.258 Ligands: UNL.4, BCL.15, U10.31 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.30 UNL.39: 5 residues within 4Å: Chain B: V.221 Chain C: I.51, W.130 Ligands: BPH.27, LDA.35 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:V.221, C:I.51, C:W.130 UNL.40: 7 residues within 4Å: Chain A: L.12 Chain C: L.168, L.286, L.287, G.289, T.290, V.291 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:L.12, C:L.286, C:L.287, C:V.291

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

PO4.6: 2 residues within 4Å: Chain A: H.126 Chain C: T.22 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Salt bridges: A:H.126 Hydrogen bonds: C:T.22, C:T.22 PO4.41: 4 residues within 4Å: Chain C: N.29, Y.52, G.54, S.55 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.29, C:Y.52, C:S.55 PO4.42: 5 residues within 4Å: Chain C: Y.4, Q.5, N.6, I.7, F.8 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.5, C:I.7, C:F.8, C:F.8

4 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)

DIO.7: 5 residues within 4Å: Chain A: E.94, F.96 Chain B: F.25, W.26, V.27 No protein-ligand interaction detected (PLIP) DIO.22: 6 residues within 4Å: Chain A: K.62, T.63, F.64 Chain B: A.199, N.200, P.201 No protein-ligand interaction detected (PLIP) DIO.23: 1 residues within 4Å: Chain B: Y.68 No protein-ligand interaction detected (PLIP) DIO.43: 3 residues within 4Å: Chain B: W.267 Chain C: F.91 Ligands: U10.17 No protein-ligand interaction detected (PLIP)

7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 3 residues within 4Å: Chain A: N.52, E.94 Chain B: A.2 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.52, A:E.94, B:A.2 EDO.9: 7 residues within 4Å: Chain A: R.177, F.178, Q.194, E.230, C.234 Chain C: G.231, R.234 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.177, A:R.177, A:Q.194, A:E.230, C:R.234 EDO.10: 6 residues within 4Å: Chain A: I.65, L.66, G.69, R.70, G.71 Chain B: E.206 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.69, A:R.70, A:G.71 EDO.11: 5 residues within 4Å: Chain A: S.80, D.82, V.115, A.116 Chain C: R.242 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.242 Water bridges: A:E.81 EDO.24: 8 residues within 4Å: Chain B: S.53, V.67, Y.68, L.81, A.82, G.84, L.86, W.87 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.53, B:Y.68, B:G.84, B:W.87 EDO.44: 6 residues within 4Å: Chain A: L.241 Chain B: C.109, I.114, Y.116 Chain C: E.3, R.229 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:E.3, C:R.229, C:R.229, B:C.109 Water bridges: B:Y.116 EDO.45: 8 residues within 4Å: Chain A: Q.194 Chain B: H.117 Chain C: Y.4, Q.5, L.225, A.226, S.228, R.229 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Y.4, C:A.226, C:S.228, C:R.229, C:R.229

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.12: 4 residues within 4Å: Chain A: Q.199, S.200, N.201, R.202 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.154, A:S.200, A:N.201, A:R.202, A:R.202 TRS.25: 2 residues within 4Å: Chain B: W.263, W.266 No protein-ligand interaction detected (PLIP)

1 x K: POTASSIUM ION(Non-covalent)

K.13: 4 residues within 4Å: Chain A: M.134, A.137, G.139, F.140 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:A.137

3 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.14: 19 residues within 4Å: Chain B: H.169, M.175, I.178, T.179, F.182, T.183 Chain C: F.68, M.123, W.158, L.161, I.180, H.183, L.184, T.187 Ligands: BCL.15, U10.17, BPH.27, BPH.29, SPN.32 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain C, Hydrophobic interactions: B:I.178, B:T.183, C:F.68, C:L.161, C:L.184 Hydrogen bonds: B:T.179, B:T.183 pi-Stacking: B:F.182 Metal complexes: C:H.183 BCL.15: 27 residues within 4Å: Chain B: F.98, A.125, I.126, A.128, Y.129, L.132, W.157, V.158, S.159, Y.163, F.168, H.169, H.174, A.177, I.178, F.181, S.245, A.246, C.248, M.249 Chain C: Y.211 Ligands: BCL.14, BPH.16, BPH.27, BCL.28, U10.31, UNL.38 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:F.98, B:F.98, B:A.125, B:A.128, B:W.157, B:Y.163, B:F.168, B:F.168, B:A.177, B:I.178, B:I.178, B:F.181, C:Y.211 Hydrogen bonds: B:S.245 Metal complexes: B:H.174 BCL.28: 19 residues within 4Å: Chain B: Y.129, L.132, F.147, I.151, H.154, L.155 Chain C: F.198, L.203, G.204, I.207, A.208, Y.211, G.212, L.215 Ligands: BCL.15, BPH.16, BPH.27, U10.31, LDA.33 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain C, Hydrophobic interactions: B:Y.129, B:L.132, B:F.147, B:L.155, C:F.198, C:I.207, C:I.207, C:Y.211, C:L.215 Metal complexes: B:H.154 pi-Stacking: C:Y.211

3 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.16: 30 residues within 4Å: Chain B: F.42, A.43, I.50, C.93, A.94, A.97, F.98, W.101, E.105, I.118, A.121, F.122, F.124, A.125, F.147, Y.149, G.150, H.154, L.239, V.242 Chain C: Y.211, A.214, L.215, A.218, M.219, W.253, M.257 Ligands: BCL.15, BCL.28, U10.31 18 PLIP interactions: 14 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:I.50, B:F.98, B:A.121, B:F.122, B:F.122, B:F.122, B:F.122, B:F.124, B:A.125, B:F.147, B:Y.149, B:L.239, B:V.242, B:V.242, C:Y.211, C:A.214, C:L.215, C:A.218 BPH.27: 28 residues within 4Å: Chain B: V.158, H.169, F.182 Chain C: W.67, M.123, A.154, L.157, W.158, L.161, T.187, N.188, F.190, S.191, H.197, F.198, L.203, S.206, I.207, L.210, Y.211, V.277, G.281, I.285 Ligands: BCL.14, BCL.15, BCL.28, BPH.29, UNL.39 17 PLIP interactions: 15 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:W.67, C:A.154, C:L.157, C:W.158, C:T.187, C:F.190, C:I.207, C:I.207, C:L.210, C:Y.211, C:V.277, B:F.182, B:F.182 Hydrogen bonds: C:H.197, C:S.206 Salt bridges: C:H.197 pi-Stacking: C:H.197 BPH.29: 25 residues within 4Å: Chain B: F.182, A.185, L.186, A.189, L.190, L.220, V.221 Chain C: S.60, L.61, G.64, W.67, F.68, A.126, V.127, W.130, T.134, T.147, A.150, F.151, A.154, A.274, T.278 Ligands: BCL.14, U10.17, BPH.27 16 PLIP interactions: 10 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:W.67, C:F.68, C:F.68, C:A.126, C:W.130, C:A.150, C:F.151, C:F.151, C:F.151, C:T.278, B:F.182, B:A.185, B:L.186, B:L.186, B:A.189, B:L.190

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

U10.17: 22 residues within 4Å: Chain B: P.172, I.176, T.179, F.180, T.183, L.190, H.191, L.194, V.195, E.213, D.214, F.217, S.224, I.225, G.226, T.227, I.230, L.233 Ligands: BCL.14, BPH.29, LDA.34, DIO.43 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:P.172, B:I.176, B:F.180, B:T.183, B:L.190, B:F.217, B:I.230, B:L.233, B:L.233 Hydrogen bonds: B:I.225, B:G.226 U10.31: 23 residues within 4Å: Chain B: F.30, G.36, W.101, R.104 Chain C: M.219, H.220, T.223, A.249, A.250, W.253, M.257, N.260, A.261, T.262, M.263, I.266, W.269, M.273 Ligands: LDA.1, BCL.15, BPH.16, BCL.28, UNL.38 13 PLIP interactions: 5 interactions with chain B, 8 interactions with chain C Hydrophobic interactions: B:F.30, B:F.30, B:F.30, B:W.101, B:W.101, C:M.219, C:W.253, C:M.257, C:A.261, C:W.269, C:W.269 Hydrogen bonds: C:T.223, C:A.261

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.26: 21 residues within 4Å: Chain A: A.16, S.19, F.20, I.22, F.23, G.26, L.27, Y.30 Chain B: N.200, P.201 Chain C: M.143, G.144, K.145, H.146, W.149, L.152, R.268, I.271, W.272, L.279 Ligands: UNL.2 19 PLIP interactions: 12 interactions with chain C, 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: C:W.149, C:W.149, C:W.149, C:I.271, C:W.272, C:L.279, A:F.20, A:I.22, A:F.23, A:F.23, A:Y.30, A:Y.30 Hydrogen bonds: C:M.143, C:K.145, B:N.200 Salt bridges: C:K.145, C:H.146, C:H.146, C:R.268

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

FE.30: 5 residues within 4Å: Chain B: H.191, H.231 Chain C: H.220, E.235, H.267 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Metal complexes: C:H.220, C:E.235, C:H.267, B:H.191, B:H.231

1 x SPN: SPEROIDENONE(Non-covalent)

SPN.32: 22 residues within 4Å: Chain C: F.68, F.69, I.71, G.72, W.76, F.86, W.116, S.120, F.121, M.123, F.124, W.158, L.161, G.162, F.163, W.172, V.176, Y.178, G.179, I.180, H.183 Ligands: BCL.14 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:F.68, C:F.68, C:W.116, C:F.121, C:F.121, C:F.124, C:W.158, C:L.161, C:F.163, C:F.163, C:F.163, C:W.172, C:V.176, C:Y.178, C:I.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kljashtorny, V.G. et al., Molecular Dynamic Studies of Reaction Centers Mutants from Rhodobacter sphaeroides and his mutant form L(M196)H+H(M202)L. CRYSTALLOGR REP. (2014)

Release Date

2014-07-16

Peptides

Reaction center protein H chain: A
Reaction center protein L chain: B
Reaction center protein M chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
M

Membrane

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

Reaction center protein L chain

Reaction center protein M chain

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