SMTL ID : 2boz.1

Photosynthetic Reaction Center Mutant With Gly M203 Replaced With Leu

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-oligomer

Ligands

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

LDA.1: 11 residues within 4Å: Chain A: Q.32, Y.40, Q.53, G.54, F.56 Chain C: R.253, G.257, F.258, W.268 Ligands: LDA.12, LDA.13 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:F.258, C:W.268, A:F.56 Hydrogen bonds: C:R.253 LDA.11: 6 residues within 4Å: Chain B: V.220 Chain C: I.50, L.60, W.129 Ligands: BCL.10, BPH.17 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.60 LDA.12: 7 residues within 4Å: Chain B: P.28, F.29 Chain C: M.256, G.257, F.258 Ligands: LDA.1, U10.19 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:F.29, C:F.258 LDA.13: 11 residues within 4Å: Chain A: W.21, L.31 Chain B: W.151 Chain C: P.200, L.203, L.204, A.207, F.208, M.272 Ligands: LDA.1, BCL.6 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:L.204, C:A.207, C:F.208, A:L.31

3 x D10: DECANE(Non-covalent)

D10.2: 5 residues within 4Å: Chain A: W.21, L.24, A.25, I.28 Ligands: D10.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.21, A:L.24, A:A.25, A:I.28 D10.3: 1 residues within 4Å: Chain A: W.21 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.21 D10.4: 2 residues within 4Å: Chain A: A.25 Ligands: D10.2 No protein-ligand interaction detected (PLIP)

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.5: 30 residues within 4Å: Chain B: 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, F.181, S.244, A.245, C.247, M.248 Chain C: Y.210 Ligands: BCL.6, BPH.7, BCL.9, BCL.10, U10.19 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:F.97, B:A.124, B:A.127, B:T.160, B:Y.162, B:F.167, B:A.176, B:I.177, B:F.180, B:F.180, B:F.181, C:Y.210 Hydrogen bonds: B:S.244 Metal complexes: B:H.173 BCL.6: 21 residues within 4Å: Chain B: I.49, Y.128, L.131, F.146, I.150, W.151, H.153, L.154, V.157 Chain C: F.197, L.203, I.206, A.207, Y.210, G.211, L.214 Ligands: BCL.5, BPH.7, BCL.10, LDA.13, U10.19 12 PLIP interactions: 6 interactions with chain C, 6 interactions with chain B, Hydrophobic interactions: C:F.197, C:I.206, C:I.206, C:Y.210, C:L.214, B:I.49, B:Y.128, B:L.131, B:F.146, B:L.154 pi-Stacking: C:Y.210 Metal complexes: B:H.153 BCL.9: 20 residues within 4Å: Chain B: H.168, M.174, I.177, S.178, F.181, T.182, L.185 Chain C: F.67, M.122, W.157, L.160, I.179, H.182, L.183, T.186 Ligands: BCL.5, U10.8, BCL.10, BPH.17, SPN.18 9 PLIP interactions: 4 interactions with chain C, 5 interactions with chain B, Hydrophobic interactions: C:F.67, C:L.160, C:L.183, B:I.177, B:I.177, B:F.181, B:L.185 Metal complexes: C:H.182 pi-Stacking: B:F.181 BCL.10: 29 residues within 4Å: Chain B: V.157, Y.162, F.181 Chain C: M.122, 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.5, BCL.6, BCL.9, LDA.11, BPH.17 15 PLIP interactions: 15 interactions with chain C, Hydrophobic interactions: C:V.126, C:A.153, 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:L.209, C:Y.210, C:V.276, C:I.284 Metal complexes: C:H.202

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.7: 31 residues within 4Å: Chain B: F.41, A.42, G.45, 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 C: Y.210, A.213, L.214, A.217, M.218, W.252, M.256 Ligands: BCL.5, BCL.6, U10.19 21 PLIP interactions: 4 interactions with chain C, 17 interactions with chain B Hydrophobic interactions: C:Y.210, C:A.213, C:L.214, C:A.217, B:A.42, B:I.49, B:A.93, B:A.96, B:A.120, B:F.121, B:F.121, B:F.123, B:A.124, B:Y.128, B:Y.148, B:I.150, B:L.238, B:V.241, B:V.241 Hydrogen bonds: B:E.104 pi-Stacking: B:F.121 BPH.17: 26 residues within 4Å: Chain B: F.181, A.184, L.185, A.188, L.189, F.216, L.219, V.220 Chain C: S.59, 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.9, BCL.10, LDA.11 15 PLIP interactions: 4 interactions with chain B, 11 interactions with chain C Hydrophobic interactions: B:F.181, B:A.184, B:A.188, B:L.189, C:W.66, C:F.67, C:F.67, C:F.67, C:W.129, C:A.149, C:F.150, C:F.150, C:A.153, C:T.277 pi-Stacking: C:F.150

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

U10.8: 21 residues within 4Å: Chain B: M.174, 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, L.232, W.263 Chain C: F.90 Ligands: BCL.9 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:F.179, B:F.179, B:F.179, B:T.182, B:L.189, B:L.193, B:F.216, B:F.216, B:Y.222, B:I.224, B:I.229, B:I.229, B:W.263, C:F.90, C:F.90 Hydrogen bonds: B:I.224, B:G.225 U10.19: 27 residues within 4Å: Chain B: F.29, Y.30, G.35, T.38, W.100, R.103 Chain C: 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.5, BCL.6, BPH.7, LDA.12 17 PLIP interactions: 14 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:L.214, C:M.218, C:H.219, 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:W.100, B:W.100 Hydrogen bonds: C:H.219, C:A.260

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

FE.14: 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

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

PO4.15: 3 residues within 4Å: Chain B: N.199 Chain C: H.145, R.267 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Salt bridges: C:H.145, C:R.267 Water bridges: A:K.62 Hydrogen bonds: B:N.199 PO4.16: 3 residues within 4Å: Chain C: N.28, G.53, S.54 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.28, C:S.54 Water bridges: C:Y.51, C:Y.51, C:L.55

1 x SPN: SPEROIDENONE(Non-covalent)

SPN.18: 25 residues within 4Å: Chain C: W.66, F.67, F.68, I.70, G.71, F.74, W.75, F.85, L.89, F.105, W.115, S.119, F.120, M.122, W.157, 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 C Hydrophobic interactions: C:W.66, C:F.67, C:F.67, C:F.67, C:I.70, C:I.70, C:F.74, C:F.74, C:F.85, C:L.89, C:W.115, C:W.157, C:L.160, 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

Potter, J.A. et al., Strong Effects of an Individual Water Molecule on the Rate of Light-Driven Charge Separation in the Rhodobacter Sphaeroides Reaction Center. J.Biol.Chem. (2005)

Release Date

2005-05-20

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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