SMTL ID : 6q53.1

CRYSTAL STRUCTURE OF THE LIGHT-HARVESTING COMPLEX II (B800-850) FROM Ectothiorhodospira haloalkaliphila

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.70 Å

Oligo State

hetero-2-2-mer

Ligands

6 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.1: 20 residues within 4Å: Chain A: L.32, F.35, L.36, A.39, H.43, V.46, F.47, Y.52, P.54 Chain B: V.23, T.26, F.27, L.30, A.31, A.34, H.35, V.38, W.41 Ligands: LYC.3, BCL.4 11 PLIP interactions: 3 interactions with chain B, 8 interactions with chain A, Hydrophobic interactions: B:F.27, B:A.34, B:W.41, A:L.32, A:F.35, A:F.35, A:V.46, A:F.47, A:F.47, A:Y.52 Metal complexes: A:H.43 BCL.2: 19 residues within 4Å: Chain A: N.11, P.12, D.15, W.19 Chain B: H.17, F.20, K.21, F.24, T.25, V.28, V.29 Chain D: Q.19, V.22, V.23, T.26 Ligands: BCL.4, DET.5, BCL.6, LYC.8 11 PLIP interactions: 5 interactions with chain D, 4 interactions with chain A, 2 interactions with chain B, Hydrophobic interactions: D:Q.19, D:V.22, D:V.23, D:T.26, A:D.15, A:W.19, B:F.20, B:V.29 Hydrogen bonds: D:Q.19, A:N.11 Metal complexes: A:D.15 BCL.4: 24 residues within 4Å: Chain A: L.18, T.34, A.39, V.42, H.43, Y.52 Chain B: F.24, F.27, V.28, A.31, H.35, V.38, W.44, F.45 Chain C: L.32, I.33, P.54, L.55 Ligands: BCL.1, BCL.2, LYC.3, DET.5, BCL.6, DET.10 12 PLIP interactions: 4 interactions with chain A, 6 interactions with chain B, 2 interactions with chain C, Hydrophobic interactions: A:L.18, A:V.42, A:Y.52, B:V.28, B:A.31, B:V.38, B:W.44, B:W.44, C:I.33, C:P.54 Hydrogen bonds: A:H.43 Metal complexes: B:H.35 BCL.6: 24 residues within 4Å: Chain C: L.32, F.35, L.36, A.39, H.43, V.46, F.47, Y.52, P.54 Chain D: V.23, T.26, F.27, L.30, A.31, A.34, H.35, V.38, W.41 Ligands: BCL.2, LYC.3, BCL.4, LYC.8, BCL.9, DET.10 11 PLIP interactions: 6 interactions with chain C, 5 interactions with chain D, Hydrophobic interactions: C:L.32, C:F.35, C:V.46, C:F.47, C:Y.52, D:V.23, D:F.27, D:A.34, D:V.38, D:W.41 Metal complexes: C:H.43 BCL.7: 12 residues within 4Å: Chain C: N.11, P.12, D.15, L.18, W.19 Chain D: H.17, F.20, K.21, F.24, T.25, V.28 Ligands: BCL.9 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain D, Hydrophobic interactions: C:N.11, C:P.12, C:L.18, C:W.19, D:F.20, D:F.24, D:V.28 Metal complexes: C:D.15, C:D.15 Salt bridges: D:K.21 BCL.9: 19 residues within 4Å: Chain C: F.35, T.38, A.39, V.42, H.43, V.46, Y.52 Chain D: F.20, F.24, F.27, V.28, H.35, V.38, W.44, F.45 Ligands: BCL.6, BCL.7, LYC.8, DET.11 14 PLIP interactions: 5 interactions with chain C, 9 interactions with chain D, Hydrophobic interactions: C:F.35, C:V.42, C:V.46, C:Y.52, D:F.20, D:F.24, D:F.27, D:V.38, D:W.44, D:W.44, D:W.44, D:F.45 Hydrogen bonds: C:H.43 Metal complexes: D:H.35

2 x LYC: LYCOPENE(Non-covalent)

LYC.3: 19 residues within 4Å: Chain A: L.32, F.35, I.41, F.45 Chain B: E.15, F.16, Q.19, F.20, V.23, F.24, F.27 Chain C: L.36, A.39, L.40, H.43, F.47 Ligands: BCL.1, BCL.4, BCL.6 21 PLIP interactions: 6 interactions with chain A, 12 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: A:L.32, A:F.35, A:F.35, A:F.35, A:I.41, A:F.45, B:E.15, B:F.16, B:F.16, B:Q.19, B:Q.19, B:F.20, B:F.20, B:F.20, B:V.23, B:F.24, B:F.24, B:F.27, C:A.39, C:H.43, C:F.47 LYC.8: 17 residues within 4Å: Chain A: K.17, L.18, V.21 Chain C: L.28, L.32, F.35, I.41, V.42 Chain D: E.15, F.16, Q.19, F.20, V.23, F.24 Ligands: BCL.2, BCL.6, BCL.9 19 PLIP interactions: 13 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:E.15, D:F.16, D:F.16, D:Q.19, D:Q.19, D:F.20, D:F.20, D:F.20, D:V.23, D:V.23, D:V.23, D:F.24, D:F.24, C:L.28, C:L.32, C:F.35, C:F.35, C:I.41, C:V.42

3 x DET: UNDECYLAMINE-N,N-DIMETHYL-N-OXIDE(Non-covalent)

DET.5: 7 residues within 4Å: Chain B: A.32, H.35, F.36, F.39, W.44 Ligands: BCL.2, BCL.4 No protein-ligand interaction detected (PLIP) DET.10: 7 residues within 4Å: Chain B: F.45 Chain D: A.34, L.37, V.38, W.41 Ligands: BCL.4, BCL.6 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:A.34, D:V.38, D:W.41, B:F.45 Hydrogen bonds: B:F.45 DET.11: 2 residues within 4Å: Chain D: H.35 Ligands: BCL.9 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leiger, K. et al., Controlling Photosynthetic Excitons by Selective Pigment Photooxidation. J.Phys.Chem.B (2019)

Release Date

2019-10-16

Peptides

light-harvesting protein subunit alpha: AC
Light-harvesting protein B:800-850 subunit beta: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
D

B
B

D
E

Membrane

We predict this structure to be a membrane protein.
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light-harvesting protein subunit alpha

Light-harvesting protein B:800-850 subunit beta