SMTL ID : 4in7.1

(M)L214N mutant of the Rhodobacter sphaeroides Reaction Center

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

hetero-1-1-1-mer

Ligands

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: A.31, Y.35, F.62 No protein-ligand interaction detected (PLIP) GOL.2: 6 residues within 4Å: Chain A: E.40, R.43, K.68 Chain B: N.200 Ligands: GOL.5, CDL.27 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.40, A:R.43, A:K.68, B:N.200 GOL.3: 4 residues within 4Å: Chain A: W.27, A.31, I.34 Ligands: GGD.7 No protein-ligand interaction detected (PLIP) GOL.4: 2 residues within 4Å: Chain A: W.27 Ligands: GOL.18 No protein-ligand interaction detected (PLIP) GOL.5: 7 residues within 4Å: Chain A: T.69, F.70 Chain B: A.199, N.200, P.201 Ligands: GOL.2, CDL.27 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:P.201, A:T.69 GOL.17: 5 residues within 4Å: Chain B: G.78, A.79, L.81, Q.88, I.89 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.79, B:A.79 GOL.18: 3 residues within 4Å: Chain B: Q.63 Ligands: GOL.4, LDA.21 No protein-ligand interaction detected (PLIP)

1 x K: POTASSIUM ION(Non-covalent)

K.6: 3 residues within 4Å: Chain A: M.140, A.143, F.146 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:M.140, A:A.143, A:F.146

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.7: 20 residues within 4Å: Chain A: Q.38, Y.46, L.48, N.58, G.60, P.61, F.62, E.100 Chain B: A.2, G.28, P.29, F.30 Chain C: R.254, M.257, G.258, F.259 Ligands: GOL.3, BCL.8, LDA.21, U10.25 10 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A, 3 interactions with chain C Hydrogen bonds: B:A.2, B:A.2, B:G.28, A:Y.46, A:N.58 Hydrophobic interactions: A:Q.38, A:F.62, C:F.259 Salt bridges: C:R.254, C:R.254

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.8: 21 residues within 4Å: Chain B: I.47, Y.129, L.132, F.147, I.151, W.152, H.154, L.155 Chain C: F.198, G.204, I.207, A.208, Y.211, G.212, N.215 Ligands: GGD.7, LDA.9, BCL.13, BCL.20, LDA.21, BPH.30 13 PLIP interactions: 8 interactions with chain B, 5 interactions with chain C, Hydrophobic interactions: B:I.47, B:Y.129, B:L.132, B:F.147, B:F.147, B:L.155, C:F.198, C:I.207, C:I.207, C:Y.211 pi-Stacking: B:H.154, C:Y.211 Metal complexes: B:H.154 BCL.13: 29 residues within 4Å: Chain B: F.98, A.125, I.126, A.128, Y.129, L.132, W.157, V.158, S.159, T.161, Y.163, N.167, F.168, H.169, H.174, A.177, I.178, F.181, F.182, S.245, A.246, C.248, M.249 Chain C: Y.211 Ligands: BCL.8, BCL.19, BCL.20, U10.25, BPH.30 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:F.98, B:F.98, B:A.125, B:T.161, B:Y.163, B:F.168, B:A.177, B:I.178, B:I.178, B:F.181, B:F.181, B:F.182, C:Y.211 Hydrogen bonds: B:S.245 Metal complexes: B:H.174 BCL.19: 21 residues within 4Å: Chain B: H.169, M.175, I.178, S.179, F.182, T.183 Chain C: F.68, L.90, M.123, W.158, L.161, V.176, I.180, H.183, L.184, T.187 Ligands: LDA.10, BCL.13, BCL.20, BPH.24, SPO.26 12 PLIP interactions: 7 interactions with chain C, 5 interactions with chain B, Hydrophobic interactions: C:F.68, C:L.90, C:L.161, C:V.176, C:I.180, C:L.184, B:I.178, B:I.178 Metal complexes: C:H.183 Hydrogen bonds: B:S.179, B:T.183 pi-Stacking: B:F.182 BCL.20: 28 residues within 4Å: Chain B: V.158, Y.163, F.182 Chain C: V.127, A.154, L.157, W.158, L.161, T.187, N.188, F.190, S.191, N.196, L.197, F.198, H.203, S.206, I.207, L.210, Y.211, V.277, G.281, I.285 Ligands: BCL.8, BCL.13, BCL.19, BPH.24, PC1.28 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain B, Hydrophobic interactions: C:V.127, C:A.154, C:L.157, C:W.158, C:T.187, C:F.190, C:L.197, C:F.198, C:I.207, C:L.210, C:Y.211, C:V.277, B:V.158 Metal complexes: C:H.203

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

LDA.9: 2 residues within 4Å: Chain B: Y.149 Ligands: BCL.8 No protein-ligand interaction detected (PLIP) LDA.10: 2 residues within 4Å: Chain B: A.173 Ligands: BCL.19 No protein-ligand interaction detected (PLIP) LDA.11: 3 residues within 4Å: Chain B: S.179, F.180 Ligands: U10.12 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.180 LDA.21: 9 residues within 4Å: Chain B: W.152 Chain C: P.201, G.204, L.205, W.269, M.273 Ligands: GGD.7, BCL.8, GOL.18 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.269 LDA.22: 5 residues within 4Å: Chain C: F.8, S.9, Q.10, W.42, F.43 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:W.42, C:F.43 pi-Cation interactions: C:W.42

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

U10.12: 16 residues within 4Å: Chain B: T.183, L.190, H.191, L.194, V.195, E.213, D.214, F.217, Y.223, S.224, I.225, G.226, T.227, I.230 Ligands: LDA.11, PC1.28 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:T.183, B:L.190, B:L.194, B:F.217, B:F.217, B:Y.223, B:I.225, B:I.230 Hydrogen bonds: B:H.191, B:D.214, B:I.225, B:G.226 U10.25: 22 residues within 4Å: Chain B: F.30, G.36, W.101, R.104 Chain C: M.219, H.220, T.223, A.249, A.250, W.253, M.257, F.259, N.260, A.261, T.262, M.263, I.266, W.269, M.273 Ligands: GGD.7, BCL.13, BPH.30 15 PLIP interactions: 12 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:M.219, C:W.253, C:M.257, C:F.259, C:F.259, C:A.261, C:I.266, C:I.266, C:W.269, C:W.269, B:F.30, B:W.101, B:W.101 Hydrogen bonds: C:T.223, C:A.261

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

PO4.14: 3 residues within 4Å: Chain B: E.73, Y.74, K.83 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.73, B:Y.74 Salt bridges: B:K.83

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

HTO.15: 4 residues within 4Å: Chain B: Q.88, T.91, I.92, W.143 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.92 Hydrogen bonds: B:Q.88 HTO.16: 1 residues within 4Å: Chain B: I.92 No protein-ligand interaction detected (PLIP)

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

FE.23: 5 residues within 4Å: Chain B: H.191, H.231 Chain C: H.220, E.235, H.267 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Metal complexes: C:H.220, C:E.235, C:H.267, B:H.191, B:H.231

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.24: 24 residues within 4Å: Chain B: F.182, A.185, L.186, A.189, L.190, L.220 Chain C: S.60, L.61, G.64, L.65, F.68, A.126, V.127, W.130, T.134, T.147, A.150, F.151, A.154, A.274, T.278 Ligands: BCL.19, BCL.20, PC1.28 13 PLIP interactions: 5 interactions with chain B, 8 interactions with chain C Hydrophobic interactions: B:F.182, B:A.185, B:L.186, B:A.189, B:L.190, C:F.68, C:W.130, C:A.150, C:F.151, C:F.151, C:A.154, C:T.278 pi-Stacking: C:F.151 BPH.30: 30 residues within 4Å: Chain B: F.42, A.43, I.50, A.94, A.97, F.98, W.101, E.105, I.118, A.121, F.122, A.125, Y.129, Y.149, H.154, S.238, L.239, V.242 Chain C: Y.211, A.214, N.215, A.218, M.219, W.253, T.256, M.257 Ligands: BCL.8, BCL.13, U10.25, MG.29 20 PLIP interactions: 16 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:A.43, B:I.50, B:A.94, B:A.97, B:F.98, B:W.101, B:A.121, B:F.122, B:F.122, B:F.122, B:Y.129, B:Y.149, B:Y.149, B:L.239, B:V.242, B:V.242, C:Y.211, C:A.214, C:A.218 Hydrogen bonds: C:N.215

1 x SPO: SPHEROIDENE(Non-covalent)

SPO.26: 20 residues within 4Å: Chain C: W.67, F.68, I.71, G.72, W.76, F.106, W.116, S.120, F.121, M.123, W.158, L.161, G.162, F.163, W.172, V.176, Y.178, I.180, H.183 Ligands: BCL.19 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:W.67, C:F.68, C:F.68, C:F.68, C:I.71, C:I.71, C:F.106, C:W.116, C:F.121, C:W.158, C:L.161, C:F.163, C:W.172, C:V.176, C:V.176, C:Y.178, C:I.180

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.27: 18 residues within 4Å: Chain A: A.22, I.28, F.29, G.32, L.33, Y.36 Chain B: N.200, P.201 Chain C: G.144, K.145, H.146, W.149, W.156, R.268, W.272, L.279 Ligands: GOL.2, GOL.5 19 PLIP interactions: 13 interactions with chain C, 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: C:W.149, C:W.149, C:W.156, C:W.156, C:W.272, C:L.279, A:I.28, A:F.29, A:F.29, A:F.29, A:Y.36 Hydrogen bonds: C:K.145, C:H.146, C:R.268, B:N.200 Salt bridges: C:H.146, C:H.146, C:H.146, C:R.268

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

PC1.28: 9 residues within 4Å: Chain B: V.221 Chain C: R.30, S.31, G.32, L.48, I.51 Ligands: U10.12, BCL.20, BPH.24 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.48, C:I.51 Hydrogen bonds: C:S.31, C:S.31, C:G.32

1 x MG: MAGNESIUM ION(Non-covalent)

MG.29: 2 residues within 4Å: Chain C: N.215 Ligands: BPH.30 No protein-ligand interaction detected (PLIP)

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 H(A) and B(A) cofactors. Biochemistry (2013)

Release Date

2013-06-05

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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