SMTL ID : 4in6.1

(M)L214A mutant of the Rhodobacter sphaeroides Reaction Center

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-oligomer

Ligands

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.1: 30 residues within 4Å: Chain A: T.38, 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, I.150, H.153, L.238, V.241 Chain B: Y.210, A.213, A.214, M.218, W.252, T.255, M.256 Ligands: BCL.3, BCL.8, U10.20 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.49, 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:Y.148, A:L.238, A:V.241, A:V.241, B:Y.210, B:A.213 Hydrogen bonds: A:E.104 BPH.19: 23 residues within 4Å: Chain A: F.181, A.184, L.185, L.189, F.216, L.219 Chain B: S.59, L.60, G.63, L.64, F.67, A.125, V.126, W.129, T.133, T.146, A.149, F.150, A.153, A.273, T.277 Ligands: BCL.14, BCL.15 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.60, B:L.64, B:F.67, B:W.129, B:A.149, B:F.150, B:F.150, B:A.153, B:T.277, A:F.181, A:A.184, A:L.189 pi-Stacking: B:F.150

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

U10.2: 16 residues within 4Å: Chain A: 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 Ligands: BCL.14, PC1.23 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:T.182, A:L.189, A:L.193, A:F.216, A:Y.222, A:I.229, A:I.229 Hydrogen bonds: A:H.190, A:D.213, A:I.224, A:G.225 U10.20: 23 residues within 4Å: Chain A: F.29, Y.30, G.35, W.100, R.103 Chain B: 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 Ligands: BPH.1, BCL.3, GGD.27 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:M.218, B:W.252, B:M.256, B:F.258, B:F.258, B:I.265, B:I.265, B:W.268, B:W.268, A:F.29, A:F.29, A:W.100 Hydrogen bonds: B:T.222, B:A.260

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.3: 29 residues within 4Å: Chain A: 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 B: Y.210 Ligands: BPH.1, BCL.8, BCL.14, BCL.15, U10.20 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:F.97, A:F.97, A:F.97, A:A.124, A:T.160, A:Y.162, A:F.167, A:A.176, A:I.177, A:F.180, A:F.180, B:Y.210 Hydrogen bonds: A:S.244 pi-Stacking: A:H.173, A:H.173 Metal complexes: A:H.173 BCL.8: 18 residues within 4Å: Chain A: Y.128, L.131, F.146, I.150, H.153, L.154, V.157 Chain B: F.197, G.203, I.206, A.207, Y.210, G.211 Ligands: BPH.1, BCL.3, GOL.12, BCL.15, LDA.16 12 PLIP interactions: 7 interactions with chain A, 5 interactions with chain B, Hydrophobic interactions: A:Y.128, A:L.131, A:F.146, A:F.146, A:L.154, A:V.157, B:F.197, B:I.206, B:I.206, B:Y.210 Metal complexes: A:H.153 pi-Stacking: B:Y.210 BCL.14: 17 residues within 4Å: Chain A: H.168, M.174, I.177, S.178, F.181, T.182 Chain B: M.122, L.160, I.179, H.182, L.183, T.186 Ligands: U10.2, BCL.3, BCL.15, BPH.19, SPO.21 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B, Hydrophobic interactions: A:I.177, A:I.177, B:L.160, B:L.183 Hydrogen bonds: A:T.182 Metal complexes: B:H.182 BCL.15: 28 residues within 4Å: Chain A: V.157, Y.162, H.168, F.181 Chain B: 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: BCL.3, BCL.8, BCL.14, BPH.19, PC1.23 14 PLIP interactions: 13 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:L.196, B:F.197, B:I.206, B:I.206, B:L.209, B:Y.210, B:V.276, A:V.157 Metal complexes: B:H.202

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

PO4.4: 3 residues within 4Å: Chain A: E.72, Y.73, K.82 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.73, A:Y.73, A:Y.73 Salt bridges: A:K.82 PO4.10: 5 residues within 4Å: Chain A: F.41, L.44, I.88, I.91, C.92 No protein-ligand interaction detected (PLIP) PO4.24: 3 residues within 4Å: Chain B: N.28, G.53, S.54 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.28, B:S.54 PO4.25: 8 residues within 4Å: Chain A: L.227, R.231 Chain B: Y.3, N.5, S.8 Chain C: M.181, A.182, M.199 7 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: B:Y.3, B:Y.3, B:N.5, B:N.5, B:Q.9, C:A.182, A:R.231 PO4.30: 8 residues within 4Å: Chain C: M.140, K.141, A.142, A.143, A.144, G.145, F.146 Ligands: GOL.33 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.141, C:A.143 Water bridges: C:K.141

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

HTO.5: 5 residues within 4Å: Chain A: Q.87, T.90, I.91, L.133, W.142 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.90, A:I.91, A:L.133

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: A.198, N.199, P.200 Chain C: K.68, T.69, F.70 Ligands: CDL.22 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:P.200, C:T.69 GOL.7: 4 residues within 4Å: Chain A: A.78, L.80, G.84, Q.87 No protein-ligand interaction detected (PLIP) GOL.9: 3 residues within 4Å: Chain A: Q.62 Ligands: LDA.16, GOL.29 No protein-ligand interaction detected (PLIP) GOL.11: 7 residues within 4Å: Chain A: S.52, V.66, Y.67, L.80, A.81, G.83, L.85 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.67, A:L.80, A:G.83 GOL.12: 4 residues within 4Å: Chain A: P.61, Y.148, I.150 Ligands: BCL.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.148 GOL.13: 6 residues within 4Å: Chain A: S.4, R.7 Chain C: E.49, E.51, D.52, G.53 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:S.4, A:R.7, C:D.52 Water bridges: A:R.7 GOL.28: 4 residues within 4Å: Chain C: W.27, A.31, I.34 Ligands: GGD.27 No protein-ligand interaction detected (PLIP) GOL.29: 2 residues within 4Å: Chain C: W.27 Ligands: GOL.9 No protein-ligand interaction detected (PLIP) GOL.31: 3 residues within 4Å: Chain C: H.134, N.135, K.138 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.135, C:K.138, C:K.138 GOL.32: 11 residues within 4Å: Chain B: S.227, R.228, F.229, G.230, R.233 Chain C: R.183, F.184, P.198, Q.200, E.236, C.240 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:G.230, B:R.233, C:R.183, C:R.183, C:Q.200, C:Q.200 GOL.33: 5 residues within 4Å: Chain C: A.143, A.144, G.145, F.146 Ligands: PO4.30 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:F.146 Water bridges: C:K.141

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

LDA.16: 8 residues within 4Å: Chain A: W.151 Chain B: P.200, L.204, F.208, W.268, M.272 Ligands: BCL.8, GOL.9 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.204, B:F.208, B:W.268 LDA.17: 5 residues within 4Å: Chain B: F.7, S.8, L.38, W.41, F.42 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.38, B:W.41, B:F.42, B:F.42 pi-Cation interactions: B:W.41 LDA.26: 7 residues within 4Å: Chain B: L.167, M.168, L.285, L.286, T.289, V.290 Chain C: L.18 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:L.285, B:L.286, B:V.290, C:L.18

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

FE.18: 5 residues within 4Å: Chain A: H.190, H.230 Chain B: H.219, E.234, H.266 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Metal complexes: A:H.190, A:H.230, B:H.219, B:E.234, B:H.266

1 x SPO: SPHEROIDENE(Non-covalent)

SPO.21: 21 residues within 4Å: Chain B: W.66, F.67, I.70, G.71, W.75, F.85, F.105, 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.14 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.105, B:W.115, B:F.120, B:W.157, B:L.160, B:F.162, B:W.171, B:V.175, B:V.175, B:Y.177, B:I.179

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.22: 17 residues within 4Å: Chain A: N.199, P.200 Chain B: G.143, K.144, H.145, W.148, W.155, R.267, W.271, L.278 Chain C: A.22, I.28, F.29, G.32, L.33, Y.36 Ligands: GOL.6 19 PLIP interactions: 15 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:W.148, B:W.148, B:W.148, B:W.155, B:W.155, B:W.271, C:F.29, C:F.29, C:L.33, C:Y.36 Hydrogen bonds: B:K.144, B:R.267 Water bridges: B:K.144 Salt bridges: B:K.144, B:H.145, B:H.145, B:H.145, B:R.267, B:R.267

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

PC1.23: 13 residues within 4Å: Chain A: V.220, G.221 Chain B: A.27, R.29, S.30, G.31, V.32, G.33, I.50, L.52, W.129 Ligands: U10.2, BCL.15 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.50, B:W.129 Hydrogen bonds: B:S.30, B:G.31

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.27: 16 residues within 4Å: Chain A: V.26, G.27, P.28 Chain B: R.253, M.256, G.257, F.258, W.268 Chain C: Q.38, Y.46, L.48, N.58, G.60, F.62 Ligands: U10.20, GOL.28 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:Q.38, C:F.62, C:F.62, B:F.258, B:F.258, B:W.268 Hydrogen bonds: C:Y.46, C:N.58 Salt bridges: B:R.253

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saer, R.G. et al., Role of Rhodobacter sphaeroides Photosynthetic Reaction Center Residue M214 in the Composition, Absorbance Properties, and Conformations of HA and BA Cofactors. Biochemistry (2013)

Release Date

2013-05-01

Peptides

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

Reaction center protein M chain

Reaction center protein H chain

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