SMTL ID : 4n7k.1

Zinc Substituted Reaction Center of the Rhodobacter sphaeroides

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

hetero-1-1-1-mer

Ligands

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: E.24, R.27, K.52 Chain B: N.199 Chain C: R.267 Ligands: GOL.16, CDL.27 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:E.24, A:R.27, C:R.267 GOL.2: 2 residues within 4Å: Chain A: A.15, Y.19 No protein-ligand interaction detected (PLIP) GOL.3: 5 residues within 4Å: Chain A: W.11, L.14, A.15 Ligands: GOL.4, GGD.5 No protein-ligand interaction detected (PLIP) GOL.4: 3 residues within 4Å: Chain A: W.11 Ligands: GOL.3, GOL.18 No protein-ligand interaction detected (PLIP) GOL.16: 7 residues within 4Å: Chain A: K.52, T.53, F.54 Chain B: A.198, N.199, P.200 Ligands: GOL.1 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:P.200 Water bridges: B:G.203, A:T.53, A:T.53 GOL.17: 6 residues within 4Å: Chain B: G.77, A.78, L.80, G.84, Q.87 Ligands: HTO.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.78, B:A.78, B:L.80 GOL.18: 3 residues within 4Å: Chain B: Q.62 Ligands: GOL.4, LDA.21 No protein-ligand interaction detected (PLIP)

1 x GGD: NONADEC-10-ENOIC ACID 2-[3,4-DIHYDROXY-6-HYDROXYMETHYL-5-(3,4,5-TRIHYDROXY-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-2-YLOXY)-TETRAHYDRO-PYRAN-2-YLOXY] -1-OCTADEC-9-ENOYLOXYMETHYL-ETHYL ESTER(Non-covalent)

GGD.5: 16 residues within 4Å: Chain A: Q.22, Y.30, N.42, G.44, F.46, E.84 Chain B: A.1, G.27, P.28, F.29 Chain C: R.253, M.256, G.257, F.258 Ligands: GOL.3, U10.25 14 PLIP interactions: 5 interactions with chain C, 5 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: C:F.258, C:F.258, C:F.258, A:Q.22, A:F.46, B:F.29 Hydrogen bonds: C:R.253, A:Y.30, A:N.42, A:E.84, B:A.1 Salt bridges: C:R.253 Water bridges: B:G.27, B:G.27

6 x 2GO: [methyl 9-acetyl-14-ethyl-20-hydroxy-4,8,13,18-tetramethyl-3-{3-oxo-3-[(3,7,11,15-tetramethylhexadec-2-en-1-yl)oxy]propyl}-3,4,20,21-tetradehydrophorbine-21-carboxylatato(2-)-kappa~4~N~23~,N~24~,N~25~,N~26~]zinc(Non-covalent)

2GO.6: 19 residues within 4Å: Chain B: I.46, Y.128, L.131, F.146, I.150, H.153, L.154, V.157 Chain C: F.197, G.203, I.206, A.207, Y.210, G.211, L.214 Ligands: LDA.7, 2GO.10, 2GO.12, LDA.21 14 PLIP interactions: 7 interactions with chain B, 7 interactions with chain C, Hydrophobic interactions: B:I.46, B:Y.128, B:L.131, B:F.146, B:F.146, B:L.154, C:F.197, C:I.206, C:I.206, C:L.214 Metal complexes: B:H.153 Hydrogen bonds: C:G.203 Water bridges: C:G.203 pi-Stacking: C:Y.210 2GO.10: 26 residues within 4Å: Chain B: A.42, 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.128, Y.148, H.153, V.241 Chain C: Y.210, A.213, L.214, M.218, W.252, M.256 Ligands: 2GO.6, 2GO.12, U10.25 18 PLIP interactions: 15 interactions with chain B, 3 interactions with chain C, Hydrophobic interactions: B:A.42, B:I.49, B:A.96, B:F.97, B:A.120, B:F.121, B:F.121, B:F.121, B:F.123, B:A.124, B:Y.128, B:Y.148, B:Y.148, B:V.241, C:Y.210, C:A.213, C:L.214 Hydrogen bonds: B:E.104 2GO.12: 29 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, S.244, A.245, C.247, M.248 Chain C: Y.210 Ligands: 2GO.6, 2GO.10, 2GO.19, 2GO.20, U10.25 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:F.97, B:F.97, B:A.124, B:A.127, B:Y.128, 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 2GO.19: 19 residues within 4Å: Chain B: H.168, M.174, I.177, S.178, F.181, T.182 Chain C: F.67, M.122, L.160, V.175, I.179, H.182, L.183, T.186 Ligands: LDA.8, 2GO.12, 2GO.20, 2GO.24, SPO.26 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain B, Hydrophobic interactions: C:F.67, C:L.160, C:V.175, C:I.179, C:L.183, B:I.177, B:I.177 Metal complexes: C:H.182 Hydrogen bonds: B:M.174, B:T.182 2GO.20: 28 residues within 4Å: Chain B: V.157, Y.162, H.168, F.181 Chain C: M.122, L.156, W.157, L.160, W.185, T.186, N.187, F.189, S.190, N.195, L.196, F.197, H.202, S.205, I.206, L.209, Y.210, V.276, G.280, I.284 Ligands: 2GO.12, 2GO.19, 2GO.24, PC1.28 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain B, Hydrophobic interactions: C:L.156, C:W.157, C:W.185, C:T.186, C:F.189, C:L.196, C:F.197, C:I.206, C:L.209, C:Y.210, C:V.276, C:I.284, B:V.157 Metal complexes: C:H.202 2GO.24: 24 residues within 4Å: Chain B: F.181, A.184, L.185, A.188, L.189, L.219, V.220 Chain C: G.63, L.64, 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: 2GO.19, 2GO.20, PC1.28 13 PLIP interactions: 9 interactions with chain C, 4 interactions with chain B, Hydrophobic interactions: C:L.64, C:F.67, C:A.125, C:W.129, C:A.149, C:F.150, C:F.150, C:A.153, B:F.181, B:A.184, B:A.188, B:L.189 pi-Stacking: C:F.150

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

LDA.7: 3 residues within 4Å: Chain B: P.61, Y.148 Ligands: 2GO.6 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.61 LDA.8: 2 residues within 4Å: Ligands: LDA.9, 2GO.19 No protein-ligand interaction detected (PLIP) LDA.9: 5 residues within 4Å: Chain B: S.178, F.179, F.243 Ligands: LDA.8, U10.11 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.179 LDA.21: 10 residues within 4Å: Chain A: W.11 Chain B: W.151 Chain C: P.200, G.203, L.204, A.207, F.208, W.268 Ligands: 2GO.6, GOL.18 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.204, C:A.207, C:F.208, C:W.268 LDA.22: 5 residues within 4Å: Chain C: F.7, L.38, L.39, W.41, F.42 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.7, C:L.38, C:L.39, C:W.41, C:F.42, C:F.42 pi-Cation interactions: C:W.41

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

U10.11: 15 residues within 4Å: Chain B: 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 Ligands: LDA.9, PC1.28 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:L.189, B:L.193, B:F.216, B:F.216, B:F.216, B:F.216, B:Y.222, B:I.224, B:I.224, B:I.229 Hydrogen bonds: B:H.190, B:I.224, B:G.225 Water bridges: B:T.226, C:E.234 U10.25: 23 residues within 4Å: Chain B: F.29, Y.30, G.35, W.100, R.103 Chain C: M.218, H.219, T.222, A.245, A.248, A.249, W.252, M.256, F.258, N.259, A.260, T.261, I.265, W.268, M.272 Ligands: GGD.5, 2GO.10, 2GO.12 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:M.218, C:W.252, C:M.256, C:F.258, C:A.260, C:I.265, C:I.265, C:W.268, C:W.268, B:F.29 Hydrogen bonds: C:T.222, C:A.260

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

PO4.13: 3 residues within 4Å: Chain B: E.72, Y.73, K.82 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.73, B:Y.73, B:Y.73 Salt bridges: B:K.82

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

HTO.14: 3 residues within 4Å: Chain B: Q.87, I.91, W.142 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.91 HTO.15: 3 residues within 4Å: Chain B: L.44, I.91 Ligands: GOL.17 No protein-ligand interaction detected (PLIP)

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

FE.23: 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 SPO: SPHEROIDENE(Non-covalent)

SPO.26: 22 residues within 4Å: Chain C: F.67, F.68, I.70, G.71, F.74, W.75, F.85, F.105, W.115, S.119, F.120, W.157, L.160, G.161, F.162, W.171, V.175, Y.177, G.178, I.179, H.182 Ligands: 2GO.19 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:F.67, C:F.67, C:F.67, C:F.68, C:I.70, C:F.74, C:F.105, C:W.115, C:F.120, C:W.157, C:L.160, C:F.162, C:W.171, C:V.175, C:V.175, C:Y.177, C:I.179

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.27: 18 residues within 4Å: Chain A: A.6, S.9, F.10, I.12, F.13, G.16, L.17, Y.20 Chain B: N.199, P.200 Chain C: G.143, K.144, H.145, W.148, R.267, W.271, L.278 Ligands: GOL.1 22 PLIP interactions: 12 interactions with chain C, 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: C:W.148, C:W.148, C:W.271, C:W.271, A:F.10, A:I.12, A:F.13, A:F.13, A:F.13, A:L.17, A:Y.20 Hydrogen bonds: C:K.144, C:H.145, C:R.267, B:N.199 Water bridges: C:K.144, A:Y.20, A:Y.20 Salt bridges: C:H.145, C:H.145, C:H.145, C:R.267

1 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.28: 13 residues within 4Å: Chain B: V.220, G.221 Chain C: S.30, G.31, V.32, G.33, L.47, I.50, L.52, W.129 Ligands: U10.11, 2GO.20, 2GO.24 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.47, C:I.50, C:W.129 Hydrogen bonds: C:S.30, C:G.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saer, R.G. et al., Structural and kinetic properties of Rhodobacter sphaeroides photosynthetic reaction centers containing exclusively Zn-coordinated bacteriochlorophyll as bacteriochlorin cofactors. Biochim.Biophys.Acta (2013)

Release Date

2014-02-05

Peptides

Reaction Center 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 H Chain

Reaction center protein L chain

Reaction center protein M chain

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