SMTL ID : 1ijd.1 (1 other biounit)

Crystallographic Structure of the LH3 Complex from Rhodopseudomonas acidophila strain 7050

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-3-3-mer

Ligands

9 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.1: 16 residues within 4Å: Chain A: P.17, L.20, G.21, A.24, A.27, H.31, V.34, W.40, Y.41 Chain B: F.23, I.26, A.27, A.30, H.31 Ligands: BOG.4, BCL.5 9 PLIP interactions: 2 interactions with chain B, 7 interactions with chain A, Hydrophobic interactions: B:A.30, A:A.24, A:V.34, A:W.40, A:Y.41, A:Y.41 Hydrogen bonds: B:H.31, A:Y.41 Metal complexes: A:H.31 BCL.2: 18 residues within 4Å: Chain A: M.1, N.2, Q.3, M.19 Chain B: V.16, I.17, T.20, R.21, A.27, A.28, H.31 Chain C: L.20 Chain D: G.19, V.22 Ligands: RPA.3, BCL.5, BCL.6, RPA.8 8 PLIP interactions: 6 interactions with chain B, 1 interactions with chain D, 1 interactions with chain A, Hydrophobic interactions: B:V.16, B:I.17, B:I.17, B:R.21, B:A.27, D:V.22, A:Q.3 Hydrogen bonds: B:R.21 BCL.5: 23 residues within 4Å: Chain A: V.23, T.26, A.27, V.30, H.31, W.40 Chain B: T.20, F.23, L.24, A.27, H.31, W.40 Chain C: V.23, F.44, L.45 Chain D: V.22, F.23 Ligands: BCL.1, BCL.2, RPA.3, BCL.6, RPA.8, BOG.9 12 PLIP interactions: 4 interactions with chain B, 2 interactions with chain D, 3 interactions with chain C, 3 interactions with chain A, Hydrophobic interactions: B:T.20, B:F.23, B:L.24, D:V.22, D:F.23, C:V.23, C:F.44, C:L.45, A:V.30, A:W.40 Metal complexes: B:H.31 Hydrogen bonds: A:H.31 BCL.6: 24 residues within 4Å: Chain A: I.6, V.10, G.15, V.23, T.26 Chain C: P.17, L.20, G.21, A.24, A.27, H.31, V.34, W.40, Y.41 Chain D: F.23, I.26, A.27, A.30, H.31 Ligands: BCL.2, RPA.3, BCL.5, BOG.9, BCL.10 13 PLIP interactions: 7 interactions with chain C, 2 interactions with chain D, 4 interactions with chain A, Hydrophobic interactions: C:A.24, C:V.34, C:W.40, C:Y.41, C:Y.41, D:A.30, A:I.6, A:V.10, A:V.23, A:T.26 Hydrogen bonds: C:Y.41, D:H.31 Metal complexes: C:H.31 BCL.7: 18 residues within 4Å: Chain C: M.1, N.2, Q.3, M.19 Chain D: V.16, I.17, T.20, R.21, A.27, A.28, H.31 Chain E: L.20 Chain F: G.19, V.22 Ligands: RPA.8, BCL.10, BCL.11, RPA.13 8 PLIP interactions: 6 interactions with chain D, 1 interactions with chain F, 1 interactions with chain C, Hydrophobic interactions: D:V.16, D:I.17, D:I.17, D:R.21, D:A.27, F:V.22, C:Q.3 Hydrogen bonds: D:R.21 BCL.10: 23 residues within 4Å: Chain C: V.23, T.26, A.27, V.30, H.31, W.40 Chain D: T.20, F.23, L.24, A.27, H.31, W.40 Chain E: V.23, F.44, L.45 Chain F: V.22, F.23 Ligands: BCL.6, BCL.7, RPA.8, BCL.11, RPA.13, BOG.14 12 PLIP interactions: 3 interactions with chain C, 2 interactions with chain F, 3 interactions with chain E, 4 interactions with chain D, Hydrophobic interactions: C:V.30, C:W.40, F:V.22, F:F.23, E:V.23, E:F.44, E:L.45, D:T.20, D:F.23, D:L.24 Hydrogen bonds: C:H.31 Metal complexes: D:H.31 BCL.11: 24 residues within 4Å: Chain C: I.6, V.10, G.15, V.23, T.26 Chain E: P.17, L.20, G.21, A.24, A.27, H.31, V.34, W.40, Y.41 Chain F: F.23, I.26, A.27, A.30, H.31 Ligands: BCL.7, RPA.8, BCL.10, BOG.14, BCL.15 13 PLIP interactions: 4 interactions with chain C, 7 interactions with chain E, 2 interactions with chain F, Hydrophobic interactions: C:I.6, C:V.10, C:V.23, C:T.26, E:A.24, E:V.34, E:W.40, E:Y.41, E:Y.41, F:A.30 Hydrogen bonds: E:Y.41, F:H.31 Metal complexes: E:H.31 BCL.12: 13 residues within 4Å: Chain E: M.1, N.2, Q.3, M.19 Chain F: V.16, I.17, T.20, R.21, A.27, A.28, H.31 Ligands: RPA.13, BCL.15 7 PLIP interactions: 1 interactions with chain E, 6 interactions with chain F, Hydrophobic interactions: E:Q.3, F:V.16, F:I.17, F:I.17, F:R.21, F:A.27 Hydrogen bonds: F:R.21 BCL.15: 15 residues within 4Å: Chain E: V.23, T.26, A.27, V.30, H.31, W.40 Chain F: T.20, F.23, L.24, A.27, H.31, W.40 Ligands: BCL.11, BCL.12, RPA.13 7 PLIP interactions: 3 interactions with chain E, 4 interactions with chain F, Hydrophobic interactions: E:V.30, E:W.40, F:T.20, F:F.23, F:L.24 Hydrogen bonds: E:H.31 Metal complexes: F:H.31

3 x RPA: RHODOPINAL GLUCOSIDE(Non-covalent)

RPA.3: 19 residues within 4Å: Chain A: L.20, V.23, T.26, V.30 Chain B: L.4, Q.8, A.9, E.11, L.12, H.15, G.19, T.20, F.23 Chain C: L.28, H.31, Y.41 Ligands: BCL.2, BCL.5, BCL.6 9 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: A:L.20, A:V.23, A:T.26, A:V.30, C:L.28, C:H.31, B:H.15 Hydrogen bonds: B:Q.8, B:Q.8 RPA.8: 26 residues within 4Å: Chain A: Q.3, K.5, I.6, T.8 Chain B: S.6 Chain C: L.20, V.23, T.26, V.30 Chain D: L.4, Q.8, A.9, E.11, L.12, H.15, G.19, T.20, F.23 Chain E: L.28, H.31, Y.41 Ligands: BCL.2, BCL.5, BCL.7, BCL.10, BCL.11 11 PLIP interactions: 4 interactions with chain C, 3 interactions with chain D, 2 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: C:L.20, C:V.23, C:T.26, C:V.30, D:H.15, E:L.28, E:H.31, A:K.5, A:I.6 Hydrogen bonds: D:Q.8, D:Q.8 RPA.13: 22 residues within 4Å: Chain C: Q.3, K.5, I.6, T.8 Chain D: S.6 Chain E: L.20, V.23, T.26, V.30 Chain F: L.4, Q.8, A.9, E.11, L.12, H.15, G.19, T.20, F.23 Ligands: BCL.7, BCL.10, BCL.12, BCL.15 9 PLIP interactions: 4 interactions with chain E, 2 interactions with chain C, 3 interactions with chain F Hydrophobic interactions: E:L.20, E:V.23, E:T.26, E:V.30, C:K.5, C:I.6, F:H.15 Hydrogen bonds: F:Q.8, F:Q.8

3 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.4: 2 residues within 4Å: Chain B: A.30 Ligands: BCL.1 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.30 Water bridges: B:L.37 BOG.9: 3 residues within 4Å: Chain D: A.30 Ligands: BCL.5, BCL.6 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:A.30 Water bridges: D:L.37 BOG.14: 3 residues within 4Å: Chain F: A.30 Ligands: BCL.10, BCL.11 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:A.30 Water bridges: F:L.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McLuskey, K. et al., The crystallographic structure of the B800-820 LH3 light-harvesting complex from the purple bacteria Rhodopseudomonas acidophila strain 7050. Biochemistry (2001)

Release Date

2001-10-17

Peptides

LIGHT-HARVESTING PROTEIN B-800/820, ALPHA CHAIN: ACE
LIGHT-HARVESTING PROTEIN B-800/820, BETA CHAIN: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

Membrane

We predict this structure to be a membrane protein.
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LIGHT-HARVESTING PROTEIN B-800/820, ALPHA CHAIN

LIGHT-HARVESTING PROTEIN B-800/820, BETA CHAIN

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