SMTL ID : 2gmr.1

Photosynthetic reaction center mutant from Rhodobacter sphaeroides with Asp L210 replaced with Asn

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-1-mer

Ligands

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.1: 21 residues within 4Å: Chain A: H.168, M.174, I.177, S.178, F.181, T.182, L.185 Chain B: W.66, M.122, W.157, L.160, I.179, H.182, L.183, W.185, T.186 Ligands: BCL.2, U10.5, BCL.8, BPH.9, SPN.11 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A, Hydrophobic interactions: B:W.66, B:L.160, B:L.183, B:W.185, A:I.177, A:I.177, A:L.185 Metal complexes: B:H.182 Hydrogen bonds: A:T.182 BCL.2: 28 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, A.245, C.247, M.248 Chain B: Y.210 Ligands: BCL.1, BCL.3, BPH.4, BCL.8, U10.10 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:F.97, A:F.97, A:A.124, A:T.160, A:Y.162, A:F.167, A:F.167, A:A.176, A:I.177, A:I.177, A:F.180, A:F.180, B:Y.210 Hydrogen bonds: A:S.244 Metal complexes: A:H.173 BCL.3: 19 residues within 4Å: Chain A: Y.128, L.131, F.146, I.150, H.153, L.154, W.156 Chain B: F.197, G.203, I.206, A.207, Y.210, G.211, L.214 Ligands: BCL.2, BPH.4, BCL.8, U10.10, LDA.12 12 PLIP interactions: 5 interactions with chain A, 7 interactions with chain B, Hydrophobic interactions: A:L.131, A:F.146, A:L.154, A:W.156, B:F.197, B:I.206, B:I.206, B:Y.210, B:L.214 Metal complexes: A:H.153 Water bridges: B:G.203 pi-Stacking: B:Y.210 BCL.8: 28 residues within 4Å: Chain A: V.157, Y.162, H.168, F.181 Chain B: 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, T.277, G.280, I.284 Ligands: BCL.1, BCL.2, BCL.3, BPH.9 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:A.153, B:L.156, B:W.157, B:T.186, B:F.189, B:F.197, B:F.197, B:I.206, B:I.206, B:L.209, B:Y.210, B:V.276, B:I.284, A:F.181 Metal complexes: B:H.202

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.4: 29 residues within 4Å: Chain A: T.38, I.89, A.93, A.96, F.97, W.100, E.104, I.117, A.120, F.121, F.123, A.124, Y.128, F.146, Y.148, G.149, I.150, H.153, V.241 Chain B: Y.210, A.213, L.214, A.217, M.218, W.252, M.256 Ligands: BCL.2, BCL.3, U10.10 19 PLIP interactions: 15 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.89, A:A.93, A:A.96, A:A.120, A:F.121, A:F.121, A:F.121, A:F.123, A:A.124, A:Y.128, A:F.146, A:Y.148, A:Y.148, A:V.241, A:V.241, B:Y.210, B:A.213, B:L.214, B:A.217 BPH.9: 25 residues within 4Å: Chain A: F.181, A.184, L.185, L.189, L.219, V.220 Chain B: L.60, G.63, L.64, F.67, F.68, A.125, V.126, W.129, T.133, T.146, A.149, F.150, A.153, A.273, V.274, T.277 Ligands: BCL.1, BCL.8, SPN.11 12 PLIP interactions: 3 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:A.184, A:L.185, A:L.189, B:L.60, B:F.67, B:F.68, B:A.149, B:F.150, B:F.150, B:F.150, B:T.277 Hydrogen bonds: B:T.133

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

U10.5: 22 residues within 4Å: Chain A: P.171, M.174, I.175, S.178, F.179, A.186, L.189, H.190, L.193, F.216, Y.222, S.223, I.224, I.229, L.232, L.246, I.250, I.254, W.259, W.262, W.263 Ligands: BCL.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:P.171, A:I.175, A:I.175, A:F.179, A:L.189, A:L.232, A:L.246, A:I.254, A:W.259, A:W.262, A:W.263 Hydrogen bonds: A:I.224 Water bridges: A:G.225 pi-Stacking: A:F.216 U10.10: 29 residues within 4Å: Chain A: F.24, V.26, G.35, T.38, F.39, W.100, R.103 Chain B: L.214, M.218, H.219, T.222, A.248, A.249, W.252, M.256, F.258, N.259, A.260, T.261, M.262, I.265, W.268, M.272 Chain C: S.93, F.96 Ligands: BCL.2, BCL.3, BPH.4, LDA.13 20 PLIP interactions: 6 interactions with chain A, 13 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: A:F.24, A:V.26, A:T.38, A:F.39, A:W.100, A:W.100, B:L.214, B:M.218, B:H.219, B:W.252, B:M.256, B:F.258, B:F.258, B:A.260, B:I.265, B:W.268, B:W.268, C:F.96 Hydrogen bonds: B:T.222, B:A.260

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

LDA.6: 8 residues within 4Å: Chain A: V.220, G.221 Chain B: S.30, G.31, V.32, G.33, G.48, I.50 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.50 Hydrogen bonds: B:G.31 LDA.12: 5 residues within 4Å: Chain B: P.200, F.208, W.268 Ligands: BCL.3, LDA.13 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.268 Water bridges: B:G.203 LDA.13: 12 residues within 4Å: Chain A: P.28 Chain B: R.253, G.257, F.258 Chain C: Q.32, Y.40, L.42, Q.53, F.56 Ligands: U10.10, LDA.12, LDA.14 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:F.258, B:F.258, B:F.258, C:F.56 Hydrogen bonds: B:R.253, B:R.253, C:Y.40 LDA.14: 4 residues within 4Å: Chain C: A.25, I.28, Y.29 Ligands: LDA.13 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:A.25, C:I.28, C:I.28, C:Y.29 pi-Cation interactions: C:Y.29

1 x FE2: FE (II) ION(Non-covalent)

FE2.7: 5 residues within 4Å: Chain A: H.190, H.230 Chain B: H.219, E.234, H.266 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Metal complexes: B:H.219, B:E.234, B:H.266, A:H.190, A:H.230

1 x SPN: SPEROIDENONE(Non-covalent)

SPN.11: 23 residues within 4Å: Chain B: W.66, F.67, F.68, I.70, G.71, F.74, W.75, F.85, W.115, S.119, F.120, M.122, W.157, L.160, G.161, F.162, W.171, V.175, Y.177, I.179, H.182 Ligands: BCL.1, BPH.9 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:W.66, B:F.67, B:F.67, B:F.67, B:I.70, B:I.70, B:F.74, B:W.115, B:F.120, B:W.157, B:L.160, B:F.162, B:F.162, B:W.171, B:V.175, B:Y.177, B:I.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hermes, S. et al., Proton uptake in the reaction center mutant L210DN from Rhodobacter sphaeroides via protonated water molecules. Biochemistry (2006)

Release Date

2006-11-21

Peptides

Photosynthetic Reaction center protein L chain: A
Photosynthetic Reaction center protein M chain: B
Photosynthetic 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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Photosynthetic Reaction center protein L chain

Photosynthetic Reaction center protein M chain

Photosynthetic reaction center protein H chain

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