SMTL ID : 7pbw.1

Cryo-EM structure of light harvesting complex 2 from Rba. sphaeroides.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-9-9-mer

Ligands

27 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)(Covalent)

BCL.1: 31 residues within 4Å: Chain A: L.20, S.21, V.24, S.27, V.28, H.31, V.34, W.40, L.41, Y.45 Chain B: I.6, W.7, V.10, G.15, L.18, F.19, A.22, A.23, A.26, I.30 Chain J: F.28, M.31, A.32, A.35, H.36, A.39 Ligands: 7OT.3, BCL.8, BCL.47, LDA.49, BCL.51 21 PLIP interactions: 10 interactions with chain A, 3 interactions with chain J, 8 interactions with chain B, Hydrophobic interactions: A:L.20, A:V.24, A:V.24, A:V.28, A:V.34, A:W.40, A:L.41, J:A.35, J:A.39, B:W.7, B:V.10, B:L.18, B:F.19, B:A.22, B:A.23, B:I.30, B:I.30 Hydrogen bonds: A:S.27, A:Y.45, J:H.36 Metal complexes: A:H.31 BCL.2: 18 residues within 4Å: Chain A: M.1, N.3, F.19 Chain I: L.20 Chain J: L.21, I.22, T.25, R.26 Chain R: G.24, V.27, M.31, A.42 Ligands: 7OT.40, BCL.44, 7OT.45, BCL.47, LDA.50, LDA.80 8 PLIP interactions: 4 interactions with chain J, 2 interactions with chain R, 2 interactions with chain A, Hydrophobic interactions: J:L.21, J:I.22, J:R.26, R:V.27, R:A.42, A:F.19, A:F.19 Hydrogen bonds: J:R.26 BCL.7: 31 residues within 4Å: Chain B: L.20, S.21, V.24, S.27, V.28, H.31, V.34, W.40, L.41, Y.45 Chain C: I.6, W.7, V.10, G.15, L.18, F.19, A.22, A.23, A.26, I.30 Chain K: F.28, M.31, A.32, A.35, H.36, A.39 Ligands: 7OT.9, BCL.13, BCL.51, LDA.53, BCL.55 22 PLIP interactions: 10 interactions with chain B, 3 interactions with chain K, 9 interactions with chain C, Hydrophobic interactions: B:L.20, B:V.24, B:V.24, B:V.28, B:V.34, B:W.40, B:L.41, K:A.35, K:A.39, C:W.7, C:V.10, C:L.18, C:F.19, C:F.19, C:A.22, C:A.23, C:I.30, C:I.30 Hydrogen bonds: B:S.27, B:Y.45, K:H.36 Metal complexes: B:H.31 BCL.8: 18 residues within 4Å: Chain A: L.20 Chain B: M.1, N.3, F.19 Chain J: G.24, V.27, M.31, L.38, A.42 Chain K: L.21, I.22, T.25, R.26 Ligands: BCL.1, 7OT.3, 7OT.45, BCL.51, LDA.54 9 PLIP interactions: 3 interactions with chain J, 2 interactions with chain B, 4 interactions with chain K, Hydrophobic interactions: J:V.27, J:L.38, J:A.42, B:F.19, B:F.19, K:L.21, K:I.22, K:R.26 Hydrogen bonds: K:R.26 BCL.12: 31 residues within 4Å: Chain C: L.20, S.21, V.24, S.27, V.28, H.31, V.34, W.40, L.41, Y.45 Chain D: I.6, W.7, V.10, G.15, L.18, F.19, A.22, A.23, A.26, I.30 Chain L: F.28, M.31, A.32, A.35, H.36, A.39 Ligands: 7OT.14, BCL.18, BCL.55, LDA.57, BCL.59 22 PLIP interactions: 10 interactions with chain C, 9 interactions with chain D, 3 interactions with chain L, Hydrophobic interactions: C:L.20, C:V.24, C:V.24, C:V.28, C:V.34, C:W.40, C:L.41, D:W.7, D:V.10, D:L.18, D:F.19, D:F.19, D:A.22, D:A.23, D:I.30, D:I.30, L:A.35, L:A.39 Hydrogen bonds: C:S.27, C:Y.45, L:H.36 Metal complexes: C:H.31 BCL.13: 17 residues within 4Å: Chain B: L.20 Chain C: M.1, N.3, F.19 Chain K: G.24, V.27, M.31, A.42 Chain L: L.21, I.22, T.25, R.26 Ligands: 7OT.3, BCL.7, 7OT.9, BCL.55, LDA.58 8 PLIP interactions: 2 interactions with chain K, 4 interactions with chain L, 2 interactions with chain C, Hydrophobic interactions: K:V.27, K:A.42, L:L.21, L:I.22, L:R.26, C:F.19, C:F.19 Hydrogen bonds: L:R.26 BCL.17: 31 residues within 4Å: Chain D: L.20, S.21, V.24, S.27, V.28, H.31, V.34, W.40, L.41, Y.45 Chain E: I.6, W.7, V.10, G.15, L.18, F.19, A.22, A.23, A.26, I.30 Chain M: F.28, M.31, A.32, A.35, H.36, A.39 Ligands: 7OT.19, LDA.20, BCL.24, BCL.59, BCL.62 22 PLIP interactions: 3 interactions with chain M, 10 interactions with chain D, 9 interactions with chain E, Hydrophobic interactions: M:A.35, M:A.39, D:L.20, D:V.24, D:V.24, D:V.28, D:V.34, D:W.40, D:L.41, E:W.7, E:V.10, E:L.18, E:F.19, E:F.19, E:A.22, E:A.23, E:I.30, E:I.30 Hydrogen bonds: M:H.36, D:S.27, D:Y.45 Metal complexes: D:H.31 BCL.18: 18 residues within 4Å: Chain C: L.20 Chain D: M.1, N.3, F.19 Chain L: G.24, V.27, M.31, A.42 Chain M: L.21, I.22, T.25, R.26 Ligands: 7OT.9, BCL.12, 7OT.14, LDA.57, BCL.59, LDA.61 8 PLIP interactions: 4 interactions with chain M, 2 interactions with chain L, 2 interactions with chain D, Hydrophobic interactions: M:L.21, M:I.22, M:R.26, L:V.27, L:A.42, D:F.19, D:F.19 Hydrogen bonds: M:R.26 BCL.23: 31 residues within 4Å: Chain E: L.20, S.21, V.24, S.27, V.28, H.31, V.34, W.40, L.41, Y.45 Chain F: I.6, W.7, V.10, G.15, L.18, F.19, A.22, A.23, A.26, I.30 Chain N: F.28, M.31, A.32, A.35, H.36, A.39 Ligands: 7OT.25, BCL.29, BCL.62, LDA.64, BCL.66 21 PLIP interactions: 10 interactions with chain E, 3 interactions with chain N, 8 interactions with chain F, Hydrophobic interactions: E:L.20, E:V.24, E:V.24, E:V.28, E:V.34, E:W.40, E:L.41, N:A.35, N:A.39, F:W.7, F:V.10, F:L.18, F:F.19, F:A.22, F:A.23, F:I.30, F:I.30 Hydrogen bonds: E:S.27, E:Y.45, N:H.36 Metal complexes: E:H.31 BCL.24: 17 residues within 4Å: Chain D: L.20 Chain E: M.1, N.3, F.19 Chain M: G.24, V.27, M.31 Chain N: L.21, I.22, T.25, R.26 Ligands: 7OT.14, BCL.17, 7OT.19, LDA.20, BCL.62, LDA.65 7 PLIP interactions: 2 interactions with chain E, 4 interactions with chain N, 1 interactions with chain M, Hydrophobic interactions: E:F.19, E:F.19, N:L.21, N:I.22, N:R.26, M:V.27 Hydrogen bonds: N:R.26 BCL.28: 30 residues within 4Å: Chain F: S.21, V.24, S.27, V.28, H.31, V.34, W.40, L.41, Y.45 Chain G: I.6, W.7, V.10, G.15, L.18, F.19, A.22, A.23, A.26, I.30 Chain O: F.28, M.31, A.32, A.35, H.36, A.39 Ligands: 7OT.30, BCL.34, BCL.66, LDA.68, BCL.70 21 PLIP interactions: 9 interactions with chain G, 3 interactions with chain O, 9 interactions with chain F, Hydrophobic interactions: G:W.7, G:V.10, G:L.18, G:F.19, G:F.19, G:A.22, G:A.23, G:I.30, G:I.30, O:A.35, O:A.39, F:V.24, F:V.24, F:V.28, F:V.34, F:W.40, F:L.41 Hydrogen bonds: O:H.36, F:S.27, F:Y.45 Metal complexes: F:H.31 BCL.29: 19 residues within 4Å: Chain E: L.20 Chain F: M.1, N.3, F.19 Chain N: G.24, V.27, M.31, L.38, A.42 Chain O: L.21, I.22, T.25, R.26 Ligands: 7OT.19, BCL.23, 7OT.25, LDA.64, BCL.66, LDA.69 9 PLIP interactions: 2 interactions with chain F, 4 interactions with chain O, 3 interactions with chain N, Hydrophobic interactions: F:F.19, F:F.19, O:L.21, O:I.22, O:R.26, N:V.27, N:L.38, N:A.42 Hydrogen bonds: O:R.26 BCL.33: 31 residues within 4Å: Chain G: L.20, S.21, V.24, S.27, V.28, H.31, V.34, W.40, L.41, Y.45 Chain H: I.6, W.7, V.10, G.15, L.18, F.19, A.22, A.23, A.26, I.30 Chain P: F.28, M.31, A.32, A.35, H.36, A.39 Ligands: 7OT.35, BCL.39, BCL.70, LDA.72, BCL.74 22 PLIP interactions: 9 interactions with chain H, 10 interactions with chain G, 3 interactions with chain P, Hydrophobic interactions: H:W.7, H:V.10, H:L.18, H:F.19, H:F.19, H:A.22, H:A.23, H:I.30, H:I.30, G:L.20, G:V.24, G:V.24, G:V.28, G:V.34, G:W.40, G:L.41, P:A.35, P:A.39 Hydrogen bonds: G:S.27, G:Y.45, P:H.36 Metal complexes: G:H.31 BCL.34: 18 residues within 4Å: Chain F: L.20 Chain G: M.1, N.3, F.19 Chain O: G.24, V.27, M.31, L.38 Chain P: L.21, I.22, T.25, R.26 Ligands: 7OT.25, BCL.28, 7OT.30, LDA.68, BCL.70, LDA.73 8 PLIP interactions: 2 interactions with chain O, 4 interactions with chain P, 2 interactions with chain G, Hydrophobic interactions: O:V.27, O:L.38, P:L.21, P:I.22, P:R.26, G:F.19, G:F.19 Hydrogen bonds: P:R.26 BCL.38: 31 residues within 4Å: Chain H: L.20, S.21, V.24, S.27, V.28, H.31, V.34, W.40, L.41, Y.45 Chain I: I.6, W.7, V.10, G.15, L.18, F.19, A.22, A.23, A.26, I.30 Chain Q: F.28, M.31, A.32, A.35, H.36, A.39 Ligands: 7OT.40, BCL.43, BCL.74, LDA.76, BCL.78 22 PLIP interactions: 9 interactions with chain I, 10 interactions with chain H, 3 interactions with chain Q, Hydrophobic interactions: I:W.7, I:V.10, I:L.18, I:F.19, I:F.19, I:A.22, I:A.23, I:I.30, I:I.30, H:L.20, H:V.24, H:V.24, H:V.28, H:V.34, H:W.40, H:L.41, Q:A.35, Q:A.39 Hydrogen bonds: H:S.27, H:Y.45, Q:H.36 Metal complexes: H:H.31 BCL.39: 19 residues within 4Å: Chain G: L.20 Chain H: M.1, N.3, F.19 Chain P: G.24, V.27, M.31, L.38, A.42 Chain Q: L.21, I.22, T.25, R.26 Ligands: 7OT.30, BCL.33, 7OT.35, LDA.72, BCL.74, LDA.77 9 PLIP interactions: 4 interactions with chain Q, 3 interactions with chain P, 2 interactions with chain H, Hydrophobic interactions: Q:L.21, Q:I.22, Q:R.26, P:V.27, P:L.38, P:A.42, H:F.19, H:F.19 Hydrogen bonds: Q:R.26 BCL.43: 18 residues within 4Å: Chain H: L.20 Chain I: M.1, N.3, F.19 Chain Q: G.24, V.27, M.31, L.38, A.42 Chain R: L.21, I.22, T.25, R.26 Ligands: 7OT.35, BCL.38, 7OT.40, BCL.78, LDA.81 9 PLIP interactions: 2 interactions with chain I, 4 interactions with chain R, 3 interactions with chain Q, Hydrophobic interactions: I:F.19, I:F.19, R:L.21, R:I.22, R:R.26, Q:V.27, Q:L.38, Q:A.42 Hydrogen bonds: R:R.26 BCL.44: 31 residues within 4Å: Chain A: I.6, W.7, V.10, G.15, L.18, F.19, A.22, A.23, A.26, I.30 Chain I: L.20, S.21, V.24, S.27, V.28, H.31, V.34, W.40, L.41, Y.45 Chain R: F.28, M.31, A.32, A.35, H.36, A.39 Ligands: BCL.2, 7OT.45, BCL.47, BCL.78, LDA.80 21 PLIP interactions: 10 interactions with chain I, 8 interactions with chain A, 3 interactions with chain R, Hydrophobic interactions: I:L.20, I:V.24, I:V.24, I:V.28, I:V.34, I:W.40, I:L.41, A:W.7, A:V.10, A:L.18, A:F.19, A:A.22, A:A.23, A:I.30, A:I.30, R:A.35, R:A.39 Hydrogen bonds: I:S.27, I:Y.45, R:H.36 Metal complexes: I:H.31 BCL.47: 21 residues within 4Å: Chain A: A.23, S.27, I.30, H.31 Chain I: V.24, Y.44, Y.45 Chain J: T.25, F.28, G.29, A.32, H.36, W.45 Chain R: V.27, F.28 Ligands: BCL.1, BCL.2, 7OT.40, BCL.44, 7OT.45, LDA.50 8 PLIP interactions: 3 interactions with chain J, 2 interactions with chain I, 2 interactions with chain R, 1 interactions with chain A, Hydrophobic interactions: J:T.25, J:W.45, I:V.24, I:Y.45, R:V.27, R:F.28, A:I.30 Metal complexes: J:H.36 BCL.51: 23 residues within 4Å: Chain A: V.24, Y.44, Y.45 Chain B: A.23, S.27, I.30, H.31, W.40 Chain J: V.27, F.28 Chain K: T.25, R.26, F.28, G.29, A.32, H.36, W.45 Ligands: BCL.1, 7OT.3, BCL.7, BCL.8, 7OT.45, LDA.54 10 PLIP interactions: 3 interactions with chain K, 3 interactions with chain B, 2 interactions with chain A, 2 interactions with chain J, Hydrophobic interactions: K:T.25, K:W.45, B:I.30, B:I.30, B:W.40, A:V.24, A:Y.45, J:V.27, J:F.28 Metal complexes: K:H.36 BCL.55: 23 residues within 4Å: Chain B: V.24, Y.44, Y.45 Chain C: A.23, S.27, I.30, H.31 Chain K: V.27, F.28 Chain L: T.25, R.26, F.28, G.29, A.32, H.36, W.45 Ligands: 7OT.3, BCL.7, 7OT.9, BCL.12, BCL.13, LDA.53, LDA.58 8 PLIP interactions: 3 interactions with chain L, 2 interactions with chain B, 1 interactions with chain C, 2 interactions with chain K, Hydrophobic interactions: L:T.25, L:W.45, B:V.24, B:Y.45, C:I.30, K:V.27, K:F.28 Metal complexes: L:H.36 BCL.59: 23 residues within 4Å: Chain C: V.24, Y.44, Y.45 Chain D: A.23, S.27, I.30, H.31, W.40 Chain L: V.27, F.28 Chain M: T.25, R.26, F.28, G.29, A.32, H.36, W.45 Ligands: 7OT.9, BCL.12, 7OT.14, BCL.17, BCL.18, LDA.61 10 PLIP interactions: 2 interactions with chain L, 3 interactions with chain D, 3 interactions with chain M, 2 interactions with chain C, Hydrophobic interactions: L:V.27, L:F.28, D:I.30, D:I.30, D:W.40, M:T.25, M:W.45, C:V.24, C:Y.45 Metal complexes: M:H.36 BCL.62: 24 residues within 4Å: Chain D: V.24, Y.44, Y.45 Chain E: A.23, S.27, I.30, H.31, W.40 Chain M: V.27, F.28 Chain N: T.25, R.26, F.28, G.29, A.32, H.36, W.45 Ligands: 7OT.14, BCL.17, 7OT.19, LDA.20, BCL.23, BCL.24, LDA.65 10 PLIP interactions: 2 interactions with chain D, 2 interactions with chain M, 3 interactions with chain N, 3 interactions with chain E, Hydrophobic interactions: D:V.24, D:Y.45, M:V.27, M:F.28, N:T.25, N:W.45, E:I.30, E:I.30, E:W.40 Metal complexes: N:H.36 BCL.66: 24 residues within 4Å: Chain E: V.24, Y.44, Y.45 Chain F: A.23, S.27, I.30, H.31, W.40 Chain N: V.27, F.28 Chain O: T.25, R.26, F.28, G.29, A.32, H.36, W.45 Ligands: 7OT.19, BCL.23, 7OT.25, BCL.28, BCL.29, LDA.64, LDA.69 9 PLIP interactions: 3 interactions with chain O, 2 interactions with chain E, 1 interactions with chain N, 3 interactions with chain F, Hydrophobic interactions: O:T.25, O:W.45, E:V.24, E:Y.45, N:V.27, F:I.30, F:I.30, F:W.40 Metal complexes: O:H.36 BCL.70: 21 residues within 4Å: Chain F: V.24, Y.44, Y.45 Chain G: A.23, S.27, I.30, H.31 Chain O: V.27, F.28 Chain P: T.25, F.28, G.29, A.32, H.36, W.45 Ligands: 7OT.25, BCL.28, 7OT.30, BCL.33, BCL.34, LDA.73 8 PLIP interactions: 1 interactions with chain O, 3 interactions with chain P, 2 interactions with chain F, 2 interactions with chain G, Hydrophobic interactions: O:V.27, P:T.25, P:W.45, F:V.24, F:Y.45, G:I.30, G:I.30 Metal complexes: P:H.36 BCL.74: 24 residues within 4Å: Chain G: V.24, Y.44, Y.45 Chain H: A.23, S.27, I.30, H.31, W.40 Chain P: V.27, F.28 Chain Q: T.25, R.26, F.28, G.29, A.32, H.36, W.45 Ligands: 7OT.30, BCL.33, 7OT.35, BCL.38, BCL.39, LDA.72, LDA.77 9 PLIP interactions: 1 interactions with chain P, 2 interactions with chain G, 3 interactions with chain H, 3 interactions with chain Q, Hydrophobic interactions: P:V.27, G:V.24, G:Y.45, H:I.30, H:I.30, H:W.40, Q:T.25, Q:W.45 Metal complexes: Q:H.36 BCL.78: 23 residues within 4Å: Chain H: V.24, Y.44, Y.45 Chain I: A.23, S.27, I.30, H.31, W.40 Chain Q: V.27, F.28 Chain R: T.25, R.26, F.28, G.29, A.32, H.36, W.45 Ligands: 7OT.35, BCL.38, 7OT.40, BCL.43, BCL.44, LDA.81 10 PLIP interactions: 3 interactions with chain R, 2 interactions with chain H, 3 interactions with chain I, 2 interactions with chain Q, Hydrophobic interactions: R:T.25, R:W.45, H:V.24, H:Y.45, I:I.30, I:I.30, I:W.40, Q:V.27, Q:F.28 Metal complexes: R:H.36

9 x 7OT: SPHEROIDENE(Non-covalent)

7OT.3: 25 residues within 4Å: Chain A: H.31, A.32, L.35, L.41, Y.45 Chain B: F.19, L.20, V.29, I.30, A.33 Chain C: N.3, K.5, I.6 Chain K: E.16, V.17, Q.20, G.24, T.25, F.28 Chain L: W.5 Ligands: BCL.1, BCL.8, BCL.13, BCL.51, BCL.55 19 PLIP interactions: 4 interactions with chain C, 6 interactions with chain B, 6 interactions with chain K, 2 interactions with chain A, 1 interactions with chain L Hydrophobic interactions: C:K.5, C:K.5, C:I.6, C:I.6, B:F.19, B:L.20, B:V.29, B:I.30, B:I.30, B:A.33, K:E.16, K:V.17, K:Q.20, K:T.25, K:F.28, K:F.28, A:H.31, A:L.35, L:W.5 7OT.9: 26 residues within 4Å: Chain B: H.31, A.32, L.35, L.41, Y.45 Chain C: F.19, L.20, V.29, I.30, A.33 Chain D: N.3, K.5, I.6 Chain L: E.16, V.17, Q.20, G.24, T.25, F.28 Chain M: W.5 Ligands: BCL.7, BCL.13, LDA.16, BCL.18, BCL.55, BCL.59 19 PLIP interactions: 2 interactions with chain B, 1 interactions with chain M, 4 interactions with chain D, 6 interactions with chain L, 6 interactions with chain C Hydrophobic interactions: B:H.31, B:L.35, M:W.5, D:K.5, D:K.5, D:I.6, D:I.6, L:E.16, L:V.17, L:Q.20, L:T.25, L:F.28, L:F.28, C:F.19, C:L.20, C:V.29, C:I.30, C:I.30, C:A.33 7OT.14: 26 residues within 4Å: Chain C: H.31, A.32, L.35, L.41, Y.45 Chain D: F.19, L.20, V.29, I.30, A.33 Chain E: N.3, K.5, I.6 Chain M: E.16, V.17, Q.20, G.24, T.25, F.28 Chain N: W.5 Ligands: BCL.12, BCL.18, LDA.22, BCL.24, BCL.59, BCL.62 18 PLIP interactions: 2 interactions with chain C, 4 interactions with chain E, 5 interactions with chain M, 6 interactions with chain D, 1 interactions with chain N Hydrophobic interactions: C:H.31, C:L.35, E:K.5, E:K.5, E:I.6, E:I.6, M:V.17, M:Q.20, M:T.25, M:F.28, M:F.28, D:F.19, D:L.20, D:V.29, D:I.30, D:I.30, D:A.33, N:W.5 7OT.19: 25 residues within 4Å: Chain D: H.31, A.32, L.35, L.41, Y.45 Chain E: F.19, L.20, V.29, I.30, A.33 Chain F: N.3, K.5, I.6 Chain N: E.16, V.17, Q.20, G.24, T.25, F.28 Chain O: W.5 Ligands: BCL.17, BCL.24, BCL.29, BCL.62, BCL.66 19 PLIP interactions: 6 interactions with chain E, 1 interactions with chain O, 6 interactions with chain N, 4 interactions with chain F, 2 interactions with chain D Hydrophobic interactions: E:F.19, E:L.20, E:V.29, E:I.30, E:I.30, E:A.33, O:W.5, N:E.16, N:V.17, N:Q.20, N:T.25, N:F.28, N:F.28, F:K.5, F:K.5, F:I.6, F:I.6, D:H.31, D:L.35 7OT.25: 25 residues within 4Å: Chain E: H.31, A.32, L.35, L.41, Y.45 Chain F: F.19, L.20, V.29, I.30, A.33 Chain G: N.3, K.5, I.6 Chain O: E.16, V.17, Q.20, G.24, T.25, F.28 Chain P: W.5 Ligands: BCL.23, BCL.29, BCL.34, BCL.66, BCL.70 19 PLIP interactions: 6 interactions with chain O, 6 interactions with chain F, 2 interactions with chain E, 1 interactions with chain P, 4 interactions with chain G Hydrophobic interactions: O:E.16, O:V.17, O:Q.20, O:T.25, O:F.28, O:F.28, F:F.19, F:L.20, F:V.29, F:I.30, F:I.30, F:A.33, E:H.31, E:L.35, P:W.5, G:K.5, G:K.5, G:I.6, G:I.6 7OT.30: 25 residues within 4Å: Chain F: H.31, A.32, L.35, L.41, Y.45 Chain G: F.19, L.20, V.29, I.30, A.33 Chain H: N.3, K.5, I.6 Chain P: E.16, V.17, Q.20, G.24, T.25, F.28 Chain Q: W.5 Ligands: BCL.28, BCL.34, BCL.39, BCL.70, BCL.74 19 PLIP interactions: 6 interactions with chain G, 6 interactions with chain P, 4 interactions with chain H, 2 interactions with chain F, 1 interactions with chain Q Hydrophobic interactions: G:F.19, G:L.20, G:V.29, G:I.30, G:I.30, G:A.33, P:E.16, P:V.17, P:Q.20, P:T.25, P:F.28, P:F.28, H:K.5, H:K.5, H:I.6, H:I.6, F:H.31, F:L.35, Q:W.5 7OT.35: 25 residues within 4Å: Chain G: H.31, A.32, L.35, L.41, Y.45 Chain H: F.19, L.20, V.29, I.30, A.33 Chain I: N.3, K.5, I.6 Chain Q: E.16, V.17, Q.20, G.24, T.25, F.28 Chain R: W.5 Ligands: BCL.33, BCL.39, BCL.43, BCL.74, BCL.78 19 PLIP interactions: 6 interactions with chain Q, 6 interactions with chain H, 1 interactions with chain R, 4 interactions with chain I, 2 interactions with chain G Hydrophobic interactions: Q:E.16, Q:V.17, Q:Q.20, Q:T.25, Q:F.28, Q:F.28, H:F.19, H:L.20, H:V.29, H:I.30, H:I.30, H:A.33, R:W.5, I:K.5, I:K.5, I:I.6, I:I.6, G:H.31, G:L.35 7OT.40: 25 residues within 4Å: Chain A: N.3, K.5, I.6 Chain H: H.31, A.32, L.35, L.41, Y.45 Chain I: F.19, L.20, V.29, I.30, A.33 Chain J: W.5 Chain R: E.16, V.17, Q.20, G.24, T.25, F.28 Ligands: BCL.2, BCL.38, BCL.43, BCL.47, BCL.78 19 PLIP interactions: 6 interactions with chain I, 6 interactions with chain R, 4 interactions with chain A, 1 interactions with chain J, 2 interactions with chain H Hydrophobic interactions: I:F.19, I:L.20, I:V.29, I:I.30, I:I.30, I:A.33, R:E.16, R:V.17, R:Q.20, R:T.25, R:F.28, R:F.28, A:K.5, A:K.5, A:I.6, A:I.6, J:W.5, H:H.31, H:L.35 7OT.45: 25 residues within 4Å: Chain A: F.19, L.20, V.29, I.30, A.33 Chain B: N.3, K.5, I.6 Chain I: H.31, A.32, L.35, Y.45 Chain J: E.16, V.17, Q.20, G.24, T.25, F.28 Chain K: W.5 Ligands: BCL.2, LDA.6, BCL.8, BCL.44, BCL.47, BCL.51 19 PLIP interactions: 6 interactions with chain J, 6 interactions with chain A, 4 interactions with chain B, 2 interactions with chain I, 1 interactions with chain K Hydrophobic interactions: J:E.16, J:V.17, J:Q.20, J:T.25, J:F.28, J:F.28, A:F.19, A:L.20, A:V.29, A:I.30, A:I.30, A:A.33, B:K.5, B:K.5, B:I.6, B:I.6, I:H.31, I:L.35, K:W.5

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

LDA.4: 8 residues within 4Å: Chain A: T.13, V.14, P.17, L.18, S.21, I.25 Chain B: K.11, V.14 Ligand excluded by PLIP LDA.5: 7 residues within 4Å: Chain A: K.11, V.14, L.18 Chain I: T.13, V.14, P.17, S.21 Ligand excluded by PLIP LDA.6: 4 residues within 4Å: Chain A: T.36, T.37 Chain I: L.35 Ligands: 7OT.45 Ligand excluded by PLIP LDA.10: 6 residues within 4Å: Chain B: T.13, V.14, S.21 Chain C: K.11, V.14 Ligands: LDA.15 Ligand excluded by PLIP LDA.11: 5 residues within 4Å: Chain A: L.35, T.36 Chain B: A.32, T.36, T.37 Ligand excluded by PLIP LDA.15: 9 residues within 4Å: Chain C: K.11, T.13, V.14, P.17, L.18, S.21 Chain D: K.11, L.18 Ligands: LDA.10 Ligand excluded by PLIP LDA.16: 5 residues within 4Å: Chain B: L.35, P.42 Chain C: T.36, T.37 Ligands: 7OT.9 Ligand excluded by PLIP LDA.20: 8 residues within 4Å: Chain D: W.40, Y.44 Chain M: A.39, A.42 Ligands: BCL.17, BCL.24, BCL.62, LDA.65 Ligand excluded by PLIP LDA.21: 8 residues within 4Å: Chain D: T.13, V.14, P.17, L.18, S.21, I.25 Chain E: K.11 Ligands: LDA.26 Ligand excluded by PLIP LDA.22: 5 residues within 4Å: Chain C: A.32 Chain D: V.29, T.36, T.37 Ligands: 7OT.14 Ligand excluded by PLIP LDA.26: 7 residues within 4Å: Chain E: T.13, V.14, L.18, S.21, I.25 Chain F: V.14 Ligands: LDA.21 Ligand excluded by PLIP LDA.27: 4 residues within 4Å: Chain D: A.32 Chain E: V.29, T.36, T.37 Ligand excluded by PLIP LDA.31: 8 residues within 4Å: Chain F: T.13, V.14, P.17, L.18, S.21, I.25 Chain G: K.11, V.14 Ligand excluded by PLIP LDA.32: 5 residues within 4Å: Chain E: L.35, T.36 Chain F: V.29, T.36, T.37 Ligand excluded by PLIP LDA.36: 8 residues within 4Å: Chain G: T.13, V.14, P.17, L.18, S.21, I.25 Chain H: V.14 Ligands: LDA.41 Ligand excluded by PLIP LDA.37: 4 residues within 4Å: Chain F: L.35, T.36 Chain G: T.36, T.37 Ligand excluded by PLIP LDA.41: 7 residues within 4Å: Chain H: T.13, V.14, S.21, I.25 Chain I: K.11, V.14 Ligands: LDA.36 Ligand excluded by PLIP LDA.42: 5 residues within 4Å: Chain G: V.28, A.32, T.36 Chain H: T.36, T.37 Ligand excluded by PLIP LDA.46: 5 residues within 4Å: Chain H: L.35, T.36 Chain I: V.29, T.36, T.37 Ligand excluded by PLIP LDA.49: 7 residues within 4Å: Chain A: Y.44 Chain J: A.35, L.38, A.39, A.42, P.44 Ligands: BCL.1 Ligand excluded by PLIP LDA.50: 5 residues within 4Å: Chain I: Y.44 Chain J: H.36 Ligands: BCL.2, BCL.47, LDA.80 Ligand excluded by PLIP LDA.53: 9 residues within 4Å: Chain B: W.40, Y.44 Chain K: A.35, L.38, A.39, A.42, T.43 Ligands: BCL.7, BCL.55 Ligand excluded by PLIP LDA.54: 6 residues within 4Å: Chain A: Y.44 Chain K: A.32, L.33, H.36 Ligands: BCL.8, BCL.51 Ligand excluded by PLIP LDA.57: 8 residues within 4Å: Chain C: W.40, Y.44 Chain L: A.35, A.42, P.44 Ligands: BCL.12, BCL.18, LDA.61 Ligand excluded by PLIP LDA.58: 4 residues within 4Å: Chain B: Y.44 Chain L: H.36 Ligands: BCL.13, BCL.55 Ligand excluded by PLIP LDA.61: 7 residues within 4Å: Chain C: Y.44 Chain M: A.32, L.33, H.36 Ligands: BCL.18, LDA.57, BCL.59 Ligand excluded by PLIP LDA.64: 10 residues within 4Å: Chain E: Y.44 Chain N: A.35, L.38, A.39, A.42, T.43 Ligands: BCL.23, BCL.29, BCL.66, LDA.69 Ligand excluded by PLIP LDA.65: 6 residues within 4Å: Chain D: Y.44 Chain N: H.36, L.46 Ligands: LDA.20, BCL.24, BCL.62 Ligand excluded by PLIP LDA.68: 10 residues within 4Å: Chain F: W.40, Y.44 Chain O: A.35, L.38, A.39, A.42, T.43 Ligands: BCL.28, BCL.34, LDA.73 Ligand excluded by PLIP LDA.69: 6 residues within 4Å: Chain E: Y.44 Chain O: H.36, L.46 Ligands: BCL.29, LDA.64, BCL.66 Ligand excluded by PLIP LDA.72: 10 residues within 4Å: Chain G: Y.44 Chain P: A.35, L.38, A.39, A.42, T.43 Ligands: BCL.33, BCL.39, BCL.74, LDA.77 Ligand excluded by PLIP LDA.73: 6 residues within 4Å: Chain F: Y.44 Chain P: H.36, L.46 Ligands: BCL.34, LDA.68, BCL.70 Ligand excluded by PLIP LDA.76: 5 residues within 4Å: Chain H: Y.44 Chain Q: A.42, T.43, P.44 Ligands: BCL.38 Ligand excluded by PLIP LDA.77: 6 residues within 4Å: Chain G: Y.44 Chain Q: H.36, L.46 Ligands: BCL.39, LDA.72, BCL.74 Ligand excluded by PLIP LDA.80: 9 residues within 4Å: Chain I: W.40, Y.44 Chain R: A.35, L.38, A.42, P.44 Ligands: BCL.2, BCL.44, LDA.50 Ligand excluded by PLIP LDA.81: 7 residues within 4Å: Chain H: Y.44 Chain R: A.32, L.33, H.36, L.46 Ligands: BCL.43, BCL.78 Ligand excluded by PLIP

9 x CA: CALCIUM ION(Non-covalent)

CA.48: 6 residues within 4Å: Chain J: A.40, T.43, P.44, W.45, L.46, G.47 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:A.40, J:T.43, J:W.45 CA.52: 6 residues within 4Å: Chain K: A.40, T.43, P.44, W.45, L.46, G.47 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:A.40, K:T.43, K:W.45, K:G.47 CA.56: 6 residues within 4Å: Chain L: A.40, T.43, P.44, W.45, L.46, G.47 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:A.40, L:T.43, L:W.45, L:G.47 CA.60: 6 residues within 4Å: Chain M: A.40, T.43, P.44, W.45, L.46, G.47 3 PLIP interactions: 3 interactions with chain M Metal complexes: M:A.40, M:T.43, M:W.45 CA.63: 6 residues within 4Å: Chain N: A.40, T.43, P.44, W.45, L.46, G.47 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:A.40, N:T.43, N:W.45, N:G.47 CA.67: 6 residues within 4Å: Chain O: A.40, T.43, P.44, W.45, L.46, G.47 3 PLIP interactions: 3 interactions with chain O Metal complexes: O:A.40, O:T.43, O:W.45 CA.71: 6 residues within 4Å: Chain P: A.40, T.43, P.44, W.45, L.46, G.47 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:A.40, P:T.43, P:W.45, P:G.47 CA.75: 6 residues within 4Å: Chain Q: A.40, T.43, P.44, W.45, L.46, G.47 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:A.40, Q:T.43, Q:W.45, Q:G.47 CA.79: 6 residues within 4Å: Chain R: A.40, T.43, P.44, W.45, L.46, G.47 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:A.40, R:T.43, R:W.45, R:G.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qian, P. et al., Cryo-EM Structure of the Rhodobacter sphaeroides Light-Harvesting 2 Complex at 2.1 angstrom. Biochemistry (2021)

Release Date

2021-11-24

Peptides

Light-harvesting protein B-800/850 alpha chain: ABCDEFGHI
Light-harvesting protein B-800/850 beta chain: JKLMNOPQR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AA

B
AB

C
AC

D
AD

E
AE

F
AF

G
AG

H
AH

I
AI

J
BA

K
BB

L
BC

M
BD

N
BE

O
BF

P
BG

Q
BH

R
BI

Membrane

We predict this structure to be a membrane protein.
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Light-harvesting protein B-800/850 alpha chain

Light-harvesting protein B-800/850 beta chain