SMTL ID : 4n7l.1

Zinc Substituted Reaction Center M(L214H) Variant of 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.5, CDL.27 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: C:R.267, B:N.199, A:R.27 GOL.2: 3 residues within 4Å: Chain A: A.15, Y.19, F.46 No protein-ligand interaction detected (PLIP) GOL.3: 2 residues within 4Å: Chain A: W.11 Ligands: GGD.6 No protein-ligand interaction detected (PLIP) GOL.4: 1 residues within 4Å: Chain A: W.11 No protein-ligand interaction detected (PLIP) GOL.5: 8 residues within 4Å: Chain A: K.52, T.53, F.54 Chain B: A.198, N.199, P.200 Ligands: GOL.1, CDL.27 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Water bridges: A:T.53, A:T.53, A:I.55, B:G.203 Hydrogen bonds: B:P.200 GOL.15: 2 residues within 4Å: Chain B: A.78, Q.87 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.78 Water bridges: B:L.80 GOL.16: 2 residues within 4Å: Chain B: Q.62 Ligands: LDA.22 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.11

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.6: 19 residues within 4Å: Chain A: Q.22, Y.30, L.32, N.42, G.44, F.46, E.84 Chain B: A.1, V.26, G.27, P.28, F.29 Chain C: R.253, M.256, G.257, F.258 Ligands: GOL.3, LDA.22, U10.25 14 PLIP interactions: 5 interactions with chain A, 6 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: A:Q.22, A:F.46, A:F.46, C:F.258, C:F.258, C:F.258, C:F.258 Hydrogen bonds: A:Y.30, A:N.42, B:A.1, B:A.1 Salt bridges: C:R.253, C:R.253 Water bridges: B:G.27

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

LDA.7: 2 residues within 4Å: Chain B: P.61, Y.148 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.61 LDA.8: 3 residues within 4Å: Chain C: F.90 Ligands: LDA.9, 2GO.20 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.90 LDA.9: 4 residues within 4Å: Chain B: S.178, F.179 Ligands: LDA.8, U10.10 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.179 LDA.22: 9 residues within 4Å: Chain A: W.11 Chain C: P.200, G.203, L.204, A.207, M.272 Ligands: GGD.6, GOL.16, 2GO.18 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:A.207 Hydrogen bonds: C:P.200 LDA.23: 4 residues within 4Å: Chain C: F.7, L.38, W.41, F.42 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.7, C:F.42

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

U10.10: 18 residues within 4Å: Chain B: T.182, L.185, 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, 2GO.17, PC1.28 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:T.182, B:L.185, B:L.189, B:L.189, B:L.193, B:F.216, B:F.216, B:Y.222, B:I.229, B:I.229 Hydrogen bonds: B:H.190, B:I.224, B:G.225 U10.25: 24 residues within 4Å: Chain B: F.29, G.35, W.100, R.103 Chain C: H.214, M.218, H.219, T.222, I.223, A.245, A.248, A.249, W.252, M.256, F.258, N.259, A.260, T.261, M.262, I.265, W.268 Ligands: GGD.6, 2GO.11, 2GO.19 14 PLIP interactions: 4 interactions with chain B, 10 interactions with chain C Hydrophobic interactions: B:F.29, B:F.29, B:W.100, B:W.100, C:M.218, C:W.252, C:F.258, C:F.258, C:A.260, C:I.265, C:W.268, C:W.268 Hydrogen bonds: C:T.222, C:A.260

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.11: 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.18, 2GO.19, 2GO.20, 2GO.21, U10.25 18 PLIP interactions: 17 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:F.97, B:F.97, B:A.124, B:A.127, B:W.156, B:V.157, B:T.160, B:Y.162, B:F.167, B:F.167, B:A.176, B:I.177, B:I.177, B:F.180, C:Y.210 Hydrogen bonds: B:S.244 pi-Cation interactions: B:H.173 Metal complexes: B:H.173 2GO.17: 23 residues within 4Å: Chain B: F.181, A.184, L.185, L.189, L.219 Chain C: L.60, G.63, 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: U10.10, 2GO.20, 2GO.21, PC1.28 10 PLIP interactions: 3 interactions with chain B, 7 interactions with chain C, Hydrophobic interactions: B:F.181, B:A.184, B:L.189, C:L.60, C:F.67, C:A.149, C:F.150, C:F.150, C:A.153 pi-Stacking: C:F.150 2GO.18: 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, H.214 Ligands: 2GO.11, 2GO.19, 2GO.21, LDA.22 12 PLIP interactions: 7 interactions with chain B, 5 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 Metal complexes: B:H.153 Hydrogen bonds: C:G.203 pi-Stacking: C:Y.210 2GO.19: 31 residues within 4Å: Chain B: F.41, 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, G.149, H.153, L.238, V.241 Chain C: Y.210, A.213, H.214, A.217, M.218, W.252, T.255, M.256 Ligands: 2GO.11, 2GO.18, U10.25 20 PLIP interactions: 16 interactions with chain B, 4 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:L.238, B:V.241, B:V.241, C:Y.210, C:A.213, C:A.217 Hydrogen bonds: B:E.104 Metal complexes: C:H.214 2GO.20: 20 residues within 4Å: Chain B: H.168, M.174, I.177, S.178, F.181, T.182 Chain C: W.66, L.89, M.122, W.157, L.160, I.179, H.182, L.183, T.186 Ligands: LDA.8, 2GO.11, 2GO.17, 2GO.21, SPO.26 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain C, Hydrophobic interactions: B:I.177, B:I.177, C:W.66, C:L.89, C:L.160, C:I.179, C:L.183 Hydrogen bonds: B:M.174 pi-Stacking: B:F.181 Metal complexes: C:H.182 2GO.21: 28 residues within 4Å: Chain B: V.157, Y.162, H.168, F.181 Chain C: A.153, L.156, W.157, L.160, 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.11, 2GO.17, 2GO.18, 2GO.20, PC1.28 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain B, Hydrophobic interactions: C:A.153, C:L.156, C:W.157, C:T.186, C:F.189, C:L.196, C:F.197, C:I.206, C:I.206, C:L.209, C:Y.210, C:V.276, B:V.157 Metal complexes: C:H.202

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

PO4.12: 3 residues within 4Å: Chain B: E.72, Y.73, K.82 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.73, B:Y.73 Salt bridges: B:K.82

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

HTO.13: 6 residues within 4Å: Chain B: Q.87, T.90, I.91, T.94, L.133, W.142 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.90, B:I.91, B:L.133 HTO.14: 3 residues within 4Å: Chain B: L.44, I.91, C.92 No protein-ligand interaction detected (PLIP)

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

FE.24: 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: 21 residues within 4Å: Chain C: F.67, F.68, I.70, G.71, 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, G.178, I.179, H.182 Ligands: 2GO.20 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:F.67, C:F.67, C:F.67, C:F.68, C:I.70, C:I.70, C:W.115, C:F.120, C:W.157, C:L.160, C:F.162, C:F.162, C:W.171, C:V.175, C:Y.177, C:I.179

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.27: 21 residues within 4Å: Chain A: A.6, F.10, I.12, F.13, A.15, G.16, L.17, Y.20 Chain B: N.199, P.200 Chain C: G.143, K.144, H.145, W.148, L.151, W.155, R.267, W.271, L.278 Ligands: GOL.1, GOL.5 26 PLIP interactions: 17 interactions with chain C, 7 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: C:W.148, C:W.148, C:W.148, C:L.151, C:W.155, C:W.155, C:W.271, C:W.271, C:L.278, A:F.10, A:I.12, A:F.13, A:A.15, A:L.17, A:Y.20, A:Y.20 Hydrogen bonds: C:K.144, C:H.145, B:N.199, B:P.200 Water bridges: C:K.144 Salt bridges: C:H.145, C:H.145, C:H.145, C:R.267, C:R.267

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

PC1.28: 12 residues within 4Å: Chain B: V.220, G.221, Y.222 Chain C: S.30, G.31, V.32, G.33, L.47, I.50 Ligands: U10.10, 2GO.17, 2GO.21 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:L.47, B:Y.222 Hydrogen bonds: C:S.30, C:G.31, C:I.50

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 (2014)

Release Date

2014-01-22

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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