SMTL ID : 3zuw.1

Photosynthetic Reaction Centre Mutant with TYR L128 replaced with HIS

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

LDA.1: 6 residues within 4Å: Chain A: A.25, Y.29 Ligands: LDA.2, LDA.3, LDA.5, LDA.17 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.29 LDA.2: 9 residues within 4Å: Chain A: W.21, L.24, A.25, I.28 Ligands: LDA.1, BCL.7, LDA.8, LDA.16, LDA.17 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.21, A:L.24, A:A.25, A:I.28 LDA.3: 3 residues within 4Å: Chain A: P.55, F.56 Ligands: LDA.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.55, A:P.55, A:F.56 LDA.4: 1 residues within 4Å: Chain A: W.21 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.21 pi-Cation interactions: A:W.21 LDA.5: 8 residues within 4Å: Chain A: F.23, G.26, L.27, Y.30 Chain C: W.271 Ligands: LDA.1, PO4.15, LDA.18 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:W.271, A:F.23, A:F.23, A:L.27, A:Y.30 LDA.8: 5 residues within 4Å: Chain B: P.28, F.29 Chain C: M.256, G.257 Ligands: LDA.2 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.29 LDA.16: 11 residues within 4Å: Chain A: W.21 Chain B: W.151 Chain C: P.200, L.204, A.207, F.208, W.268, M.272 Ligands: LDA.2, BCL.7, LDA.17 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:A.207, C:F.208, C:W.268 LDA.17: 12 residues within 4Å: Chain A: Q.32, Y.40, L.42, Q.53, F.56 Chain C: G.257, F.258, W.268 Ligands: LDA.1, LDA.2, LDA.16, U10.21 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Water bridges: A:Y.40 Hydrophobic interactions: C:F.258, C:W.268 LDA.18: 9 residues within 4Å: Chain C: H.145, W.148, L.151, I.270, W.271, V.274, L.278 Ligands: LDA.5, PO4.15 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:W.148, C:L.151, C:I.270, C:W.271, C:V.274, C:L.278

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.6: 29 residues within 4Å: Chain B: F.97, A.124, I.125, A.127, H.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 C: Y.210 Ligands: BCL.7, BPH.9, BCL.11, BCL.12, U10.21 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:F.97, B:F.97, B:F.97, B:F.97, B:A.124, B:A.127, B:V.157, B:T.160, B:Y.162, B:F.167, B:A.176, B:I.177, B:F.180, B:F.180, C:Y.210 Hydrogen bonds: B:S.244 Metal complexes: B:H.173 BCL.7: 19 residues within 4Å: Chain B: H.128, L.131, F.146, I.150, H.153, L.154 Chain C: F.197, G.203, I.206, A.207, Y.210, G.211, L.214 Ligands: LDA.2, BCL.6, BPH.9, BCL.12, LDA.16, U10.21 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain C, Hydrophobic interactions: B:L.131, B:F.146, B:L.154, C:F.197, C:I.206, C:I.206, C:Y.210, C:L.214 Hydrogen bonds: B:H.128 Metal complexes: B:H.153 BCL.11: 20 residues within 4Å: Chain B: H.168, M.174, I.177, S.178, T.182 Chain C: W.66, F.67, M.122, W.157, L.160, V.175, I.179, H.182, L.183, T.186 Ligands: BCL.6, U10.10, BCL.12, BPH.19, SPN.20 10 PLIP interactions: 3 interactions with chain B, 7 interactions with chain C, Hydrophobic interactions: B:I.177, B:I.177, C:W.66, C:F.67, C:L.160, C:V.175, C:I.179, C:L.183 pi-Stacking: B:F.181 Metal complexes: C:H.182 BCL.12: 27 residues within 4Å: Chain B: V.157, Y.162, H.168, F.181 Chain C: 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, Y.210, V.276, T.277, G.280, I.284 Ligands: BCL.6, BCL.7, BCL.11, BPH.19 12 PLIP interactions: 12 interactions with chain C, Hydrophobic interactions: C:L.156, C:W.157, C:T.186, C:F.189, C:L.196, C:F.197, C:F.197, C:I.206, C:Y.210, C:V.276, C:I.284 Metal complexes: C:H.202

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.9: 28 residues within 4Å: Chain B: 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.148, G.149, I.150, H.153, V.241 Chain C: Y.210, A.213, L.214, A.217, M.218, W.252, T.255, M.256 Ligands: BCL.6, BCL.7, U10.21 17 PLIP interactions: 14 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:I.49, B:A.96, B:A.120, B:F.121, B:F.121, B:F.123, B:A.124, B:Y.148, B:Y.148, B:I.150, B:V.241, B:V.241, C:Y.210, C:A.213, C:A.217 Hydrogen bonds: B:E.104 pi-Stacking: B:F.121 BPH.19: 24 residues within 4Å: Chain B: F.181, A.184, L.185, A.188, L.189, L.219, V.220 Chain C: 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.11, BCL.12 13 PLIP interactions: 10 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:W.66, C:F.67, C:W.129, C:W.129, C:A.149, C:F.150, C:F.150, C:F.150, C:A.153, B:F.181, B:A.184, B:A.188 pi-Stacking: C:F.150

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

U10.10: 19 residues within 4Å: Chain B: I.175, S.178, F.179, T.182, L.189, H.190, L.193, V.194, E.212, D.213, F.216, Y.222, S.223, I.224, G.225, T.226, I.229 Chain C: F.90 Ligands: BCL.11 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:I.175, B:F.179, B:F.179, B:T.182, B:L.189, B:L.193, B:F.216, B:F.216, B:F.216, B:I.224, B:I.229, C:F.90 Hydrogen bonds: B:I.224, B:G.225 U10.21: 26 residues within 4Å: Chain B: F.29, Y.30, G.35, T.38, W.100, R.103 Chain C: 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.6, BCL.7, BPH.9, LDA.17 17 PLIP interactions: 12 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:M.218, C:W.252, C:M.256, C:F.258, C:F.258, C:A.260, C:I.265, C:I.265, C:W.268, C:W.268, B:F.29, B:F.29, B:F.29, B:W.100, B:W.100 Hydrogen bonds: C:H.219, C:A.260

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

FE.13: 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:E.234, C:E.234, C:H.266

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

PO4.14: 3 residues within 4Å: Chain C: N.28, G.53, S.54 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.28, C:S.54, C:S.54 PO4.15: 5 residues within 4Å: Chain B: N.199 Chain C: H.145, R.267 Ligands: LDA.5, LDA.18 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

1 x SPN: SPEROIDENONE(Non-covalent)

SPN.20: 22 residues within 4Å: Chain C: F.67, F.68, I.70, G.71, F.74, W.75, W.115, S.119, F.120, M.122, F.123, W.157, L.160, G.161, F.162, W.171, V.175, Y.177, G.178, I.179, H.182 Ligands: BCL.11 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:F.67, C:F.67, C:F.67, C:I.70, C:I.70, C:F.74, C:F.74, C:W.115, C:F.120, C:F.123, C:W.157, C:L.160, C:F.162, C:F.162, C:W.171, C:V.175, C:V.175, C:I.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gibasiewicz, K. et al., Mechanism of Recombination of the P(+)H(A)(-) Radical Pair in Mutant Rhodobacter Sphaeroides Reaction Centers with Modified Free Energy Gaps between P(+)B(A)(-) and P(+)H(A)(-). J Phys Chem B (2011)

Release Date

2011-11-16

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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