SMTL ID : 3v3z.1

I(L177)H mutant structure of photosynthetic reaction center from Rhodobacter sphaeroides

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

LDA.1: 6 residues within 4Å: Chain A: F.14, G.17, L.18, Y.21 Ligands: LDA.22, PO4.24 No protein-ligand interaction detected (PLIP) LDA.20: 8 residues within 4Å: Chain A: W.12 Chain B: W.151 Chain C: P.200, F.208, W.268, M.272 Ligands: BCL.10, LDA.21 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:F.208, C:W.268, A:W.12 LDA.21: 9 residues within 4Å: Chain A: Q.23, Y.31, G.45, F.47 Chain C: R.253, G.257, F.258 Ligands: U10.18, LDA.20 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:F.47, C:F.258, C:F.258, C:F.258 Hydrogen bonds: C:R.253 LDA.22: 5 residues within 4Å: Chain C: W.148, W.271, L.278 Ligands: LDA.1, PO4.24 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:W.148, C:W.148, C:W.271 pi-Cation interactions: C:H.145, C:W.148 LDA.23: 4 residues within 4Å: Chain C: F.7, T.8, W.41, F.42 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.7, C:F.7, C:F.42 pi-Cation interactions: C:W.41

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

PO4.2: 2 residues within 4Å: Chain A: H.117 Chain C: T.21 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Salt bridges: A:H.117 Hydrogen bonds: C:T.21 PO4.3: 2 residues within 4Å: Chain A: N.192, R.193 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.193 PO4.24: 5 residues within 4Å: Chain B: N.199 Chain C: H.145, R.267 Ligands: LDA.1, LDA.22 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Salt bridges: C:H.145, C:R.267 Hydrogen bonds: B:N.199 PO4.25: 5 residues within 4Å: Chain B: E.201 Chain C: Y.134, M.142, G.143, K.144 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.144 Salt bridges: C:K.144 PO4.26: 4 residues within 4Å: Chain C: N.28, Y.51, G.53, S.54 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.28, C:Y.51, C:S.54, C:S.54

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

HTO.4: 4 residues within 4Å: Chain A: D.73, A.107 Chain C: D.240, R.241 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Water bridges: C:R.241 Hydrogen bonds: A:A.107 HTO.5: 4 residues within 4Å: Chain A: G.118, H.119, N.120, K.123 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.119, A:N.120, A:K.123, A:K.123 HTO.13: 5 residues within 4Å: Chain A: E.34, D.37, G.38 Chain B: S.4, R.7 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.7, A:E.34 Water bridges: B:K.8, A:E.72

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

DIO.6: 8 residues within 4Å: Chain A: R.168, F.169, Q.185, E.221, C.225 Chain C: S.227, G.230, R.233 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.233, A:Q.185 DIO.14: 1 residues within 4Å: Chain B: W.262 No protein-ligand interaction detected (PLIP)

1 x K: POTASSIUM ION(Non-covalent)

K.7: 4 residues within 4Å: Chain A: M.125, A.128, G.130, F.131 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:A.128, A:F.131

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.8: 18 residues within 4Å: Chain B: H.168, M.174, H.177, T.178, F.181, T.182 Chain C: L.89, M.122, L.160, I.179, H.182, L.183, T.186 Ligands: BCL.9, U10.12, BCL.15, BPH.16, SPN.19 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain B, Hydrophobic interactions: C:L.89, C:L.160, C:I.179, C:L.183, B:F.181, B:T.182 Metal complexes: C:H.182 BCL.9: 28 residues within 4Å: Chain B: F.97, A.124, I.125, A.127, Y.128, L.131, W.156, V.157, S.158, G.161, Y.162, N.166, F.167, H.168, H.173, A.176, H.177, F.180, S.244, A.245, C.247, M.248 Chain C: Y.210 Ligands: BCL.8, BCL.10, BPH.11, BCL.15, U10.18 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:F.97, B:A.124, B:A.127, B:V.157, B:Y.162, B:F.167, B:F.167, B:A.176, B:F.180, B:F.180, C:Y.210 Hydrogen bonds: B:S.244 Metal complexes: B:H.173 BCL.10: 18 residues within 4Å: Chain B: Y.128, L.131, F.146, I.150, W.151, H.153, L.154 Chain C: G.203, I.206, A.207, Y.210, G.211, L.214 Ligands: BCL.9, BPH.11, BCL.15, U10.18, LDA.20 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain C, Hydrophobic interactions: B:L.131, B:F.146, B:L.154, C:I.206, C:I.206, C:L.214 Metal complexes: B:H.153 pi-Stacking: C:Y.210 BCL.15: 27 residues within 4Å: Chain B: V.157, Y.162, F.181 Chain C: 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, T.277, G.280, I.284 Ligands: BCL.8, BCL.9, BCL.10, BPH.16 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain B, Hydrophobic interactions: C:V.126, C:L.156, C:W.157, C:T.186, C:F.189, C:L.196, C:I.206, C:L.209, C:Y.210, C:V.276, C:T.277, B:F.181 Metal complexes: C:H.202

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.11: 26 residues within 4Å: Chain B: I.49, A.93, A.96, F.97, W.100, E.104, I.117, A.120, F.121, A.124, Y.128, Y.148, G.149, I.150, H.153, L.238, V.241 Chain C: Y.210, A.213, L.214, M.218, W.252, M.256 Ligands: BCL.9, BCL.10, U10.18 16 PLIP interactions: 3 interactions with chain C, 13 interactions with chain B Hydrophobic interactions: C:Y.210, C:A.213, C:L.214, B:I.49, B:A.96, B:A.120, B:F.121, B:F.121, B:F.121, B:F.121, B:A.124, B:Y.128, B:Y.148, B:L.238, B:V.241 Hydrogen bonds: B:E.104 BPH.16: 18 residues within 4Å: Chain B: F.181, L.185, L.189, L.219 Chain C: L.60, G.63, L.64, F.67, A.125, V.126, W.129, T.146, A.149, F.150, A.153, T.277 Ligands: BCL.8, BCL.15 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:F.181, B:L.185, B:L.189, C:L.64, C:F.67, C:F.150, C:F.150, C:T.277 pi-Stacking: C:F.150

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

U10.12: 16 residues within 4Å: Chain B: I.175, T.178, F.179, L.185, L.189, H.190, L.193, F.216, Y.222, S.223, I.224, G.225, T.226, I.229, L.232 Ligands: BCL.8 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:T.178, B:F.179, B:L.185, B:F.216, B:Y.222, B:I.224, B:L.232 Hydrogen bonds: B:I.224, B:G.225 pi-Stacking: B:F.216 U10.18: 21 residues within 4Å: Chain B: F.29, G.35, T.38, W.100 Chain C: M.218, H.219, T.222, A.248, A.249, W.252, M.256, F.258, N.259, A.260, I.265, W.268, M.272 Ligands: BCL.9, BCL.10, BPH.11, LDA.21 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:M.218, C:W.252, C:M.256, C:F.258, C:W.268, B:F.29, B:T.38, B:W.100, B:W.100 Hydrogen bonds: C:A.260

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

FE.17: 5 residues within 4Å: Chain B: H.190, H.230 Chain C: H.219, E.234, H.266 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Metal complexes: B:H.190, B:H.230, C:H.219, C:E.234, C:H.266

1 x SPN: SPEROIDENONE(Non-covalent)

SPN.19: 22 residues within 4Å: Chain C: F.67, F.68, I.70, G.71, W.75, F.85, F.105, W.115, L.116, S.119, F.120, M.122, W.157, L.160, G.161, F.162, V.175, Y.177, G.178, I.179, H.182 Ligands: BCL.8 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:F.67, C:F.67, C:F.67, C:I.70, C:F.105, C:W.115, C:L.116, C:W.157, C:L.160, C:F.162, C:F.162, C:V.175, C:V.175, C:Y.177, C:Y.177, C:I.179

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

CL.27: 5 residues within 4Å: Chain C: Y.3, Q.4, N.5, I.6, F.7 Ligand excluded by PLIP

Links

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Citation

Vasilieva, L.G. et al., The site-directed mutation I(L177)H in Rhodobacter sphaeroides reaction center affects coordination of P(A) and B(B) bacteriochlorophylls. Biochim.Biophys.Acta (2012)

Release Date

2012-03-14

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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