SMTL ID : 6zxa.1

LH2 complex from Marichromatium purpuratum

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-7-7-mer

Ligands

21 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.1: 16 residues within 4Å: Chain A: H.17, P.18, D.21, W.25 Chain B: H.20, W.23, K.24, V.27, V.31 Chain C: M.7 Chain N: H.25 Ligands: QS2.2, BCL.4, QSE.6, QSE.33, BCL.34 4 PLIP interactions: 4 interactions with chain A, Hydrophobic interactions: A:P.18, A:W.25 pi-Stacking: A:H.17 Metal complexes: A:D.21 BCL.3: 21 residues within 4Å: Chain A: F.38, L.41, F.42, M.45, H.49, A.52, Y.58, F.60 Chain B: S.29, W.30, I.33, A.34, V.37, H.38, T.41 Chain C: I.48 Ligands: BCL.4, QS2.5, BCL.7, BCL.9, QSE.10 9 PLIP interactions: 7 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, Hydrophobic interactions: A:F.38, A:L.41, A:F.42, A:F.42, A:A.52, A:Y.58, C:I.48, B:V.37 Metal complexes: A:H.49 BCL.4: 21 residues within 4Å: Chain A: L.41, Q.44, M.45, I.48, H.49, A.52, Y.58 Chain B: W.30, V.31, A.34, S.35, H.38, V.39, W.42, W.47, F.48 Chain M: F.60 Ligands: BCL.1, BCL.3, QSE.6, BCL.34 15 PLIP interactions: 10 interactions with chain B, 3 interactions with chain A, 2 interactions with chain M, Hydrophobic interactions: B:W.30, B:W.30, B:A.34, B:H.38, B:W.42, B:W.47, B:W.47, B:F.48, A:I.48, A:Y.58, M:F.60, M:F.60 Salt bridges: B:H.38 Metal complexes: B:H.38 Hydrogen bonds: A:Q.44 BCL.7: 16 residues within 4Å: Chain B: H.25 Chain C: H.17, P.18, D.21, W.25 Chain D: H.20, W.23, K.24, V.27, V.31 Chain E: M.7 Ligands: BCL.3, QS2.5, QSE.6, BCL.9, QSE.10 4 PLIP interactions: 4 interactions with chain C, Hydrophobic interactions: C:P.18, C:W.25 pi-Stacking: C:H.17 Metal complexes: C:D.21 BCL.8: 21 residues within 4Å: Chain C: F.38, L.41, F.42, M.45, H.49, A.52, Y.58, F.60 Chain D: S.29, W.30, I.33, A.34, V.37, H.38, T.41 Chain E: I.48 Ligands: BCL.9, BCL.11, QS2.12, QSE.13, BCL.15 9 PLIP interactions: 7 interactions with chain C, 1 interactions with chain E, 1 interactions with chain D, Hydrophobic interactions: C:F.38, C:L.41, C:F.42, C:F.42, C:A.52, C:Y.58, E:I.48, D:V.37 Metal complexes: C:H.49 BCL.9: 21 residues within 4Å: Chain A: F.60 Chain C: L.41, Q.44, M.45, I.48, H.49, A.52, Y.58 Chain D: W.30, V.31, A.34, S.35, H.38, V.39, W.42, W.47, F.48 Ligands: BCL.3, BCL.7, BCL.8, QSE.10 15 PLIP interactions: 10 interactions with chain D, 4 interactions with chain C, 1 interactions with chain A, Hydrophobic interactions: D:W.30, D:W.30, D:A.34, D:H.38, D:W.42, D:W.47, D:W.47, D:F.48, C:I.48, C:A.52, C:Y.58, A:F.60 Salt bridges: D:H.38 Metal complexes: D:H.38 Hydrogen bonds: C:Q.44 BCL.11: 16 residues within 4Å: Chain D: H.25 Chain E: H.17, P.18, D.21, W.25 Chain F: H.20, W.23, K.24, V.27, V.31 Chain G: M.7 Ligands: BCL.8, QSE.10, QS2.12, QSE.13, BCL.15 3 PLIP interactions: 3 interactions with chain E, Hydrophobic interactions: E:P.18, E:W.25 Metal complexes: E:D.21 BCL.14: 21 residues within 4Å: Chain E: F.38, L.41, F.42, M.45, H.49, A.52, Y.58, F.60 Chain F: S.29, W.30, I.33, A.34, V.37, H.38, T.41 Chain G: I.48 Ligands: BCL.15, BCL.16, QS2.17, QSE.18, BCL.20 9 PLIP interactions: 1 interactions with chain G, 7 interactions with chain E, 1 interactions with chain F, Hydrophobic interactions: G:I.48, E:F.38, E:L.41, E:F.42, E:F.42, E:A.52, E:Y.58, F:V.37 Metal complexes: E:H.49 BCL.15: 21 residues within 4Å: Chain C: F.60 Chain E: L.41, Q.44, M.45, I.48, H.49, A.52, Y.58 Chain F: W.30, V.31, A.34, S.35, H.38, V.39, W.42, W.47, F.48 Ligands: BCL.8, BCL.11, QSE.13, BCL.14 15 PLIP interactions: 10 interactions with chain F, 4 interactions with chain E, 1 interactions with chain C, Hydrophobic interactions: F:W.30, F:W.30, F:A.34, F:H.38, F:W.42, F:W.47, F:W.47, F:F.48, E:I.48, E:A.52, E:Y.58, C:F.60 Salt bridges: F:H.38 Metal complexes: F:H.38 Hydrogen bonds: E:Q.44 BCL.16: 16 residues within 4Å: Chain F: H.25 Chain G: H.17, P.18, D.21, W.25 Chain H: H.20, W.23, K.24, V.27, V.31 Chain I: M.7 Ligands: QSE.13, BCL.14, QS2.17, QSE.18, BCL.20 3 PLIP interactions: 3 interactions with chain G, Hydrophobic interactions: G:P.18, G:W.25 Metal complexes: G:D.21 BCL.19: 21 residues within 4Å: Chain G: F.38, L.41, F.42, M.45, H.49, A.52, Y.58, F.60 Chain H: S.29, W.30, I.33, A.34, V.37, H.38, T.41 Chain I: I.48 Ligands: BCL.20, BCL.21, QS2.22, QSE.23, BCL.25 9 PLIP interactions: 7 interactions with chain G, 1 interactions with chain I, 1 interactions with chain H, Hydrophobic interactions: G:F.38, G:L.41, G:F.42, G:F.42, G:A.52, G:Y.58, I:I.48, H:V.37 Metal complexes: G:H.49 BCL.20: 21 residues within 4Å: Chain E: F.60 Chain G: L.41, Q.44, M.45, I.48, H.49, A.52, Y.58 Chain H: W.30, V.31, A.34, S.35, H.38, V.39, W.42, W.47, F.48 Ligands: BCL.14, BCL.16, QSE.18, BCL.19 16 PLIP interactions: 4 interactions with chain G, 2 interactions with chain E, 10 interactions with chain H, Hydrophobic interactions: G:I.48, G:A.52, G:Y.58, E:F.60, E:F.60, H:W.30, H:W.30, H:A.34, H:H.38, H:W.42, H:W.47, H:W.47, H:F.48 Hydrogen bonds: G:Q.44 Salt bridges: H:H.38 Metal complexes: H:H.38 BCL.21: 16 residues within 4Å: Chain H: H.25 Chain I: H.17, P.18, D.21, W.25 Chain J: H.20, W.23, K.24, V.27, V.31 Chain K: M.7 Ligands: QSE.18, BCL.19, QS2.22, QSE.23, BCL.25 3 PLIP interactions: 3 interactions with chain I, Hydrophobic interactions: I:P.18, I:W.25 Metal complexes: I:D.21 BCL.24: 21 residues within 4Å: Chain I: F.38, L.41, F.42, M.45, H.49, A.52, Y.58, F.60 Chain J: S.29, W.30, I.33, A.34, V.37, H.38, T.41 Chain K: I.48 Ligands: BCL.25, BCL.26, QS2.27, BCL.29, QSE.30 9 PLIP interactions: 1 interactions with chain J, 7 interactions with chain I, 1 interactions with chain K, Hydrophobic interactions: J:V.37, I:F.38, I:L.41, I:F.42, I:F.42, I:A.52, I:Y.58, K:I.48 Metal complexes: I:H.49 BCL.25: 21 residues within 4Å: Chain G: F.60 Chain I: L.41, Q.44, M.45, I.48, H.49, A.52, Y.58 Chain J: W.30, V.31, A.34, S.35, H.38, V.39, W.42, W.47, F.48 Ligands: BCL.19, BCL.21, QSE.23, BCL.24 15 PLIP interactions: 4 interactions with chain I, 10 interactions with chain J, 1 interactions with chain G, Hydrophobic interactions: I:I.48, I:A.52, I:Y.58, J:W.30, J:W.30, J:A.34, J:H.38, J:W.42, J:W.47, J:W.47, J:F.48, G:F.60 Hydrogen bonds: I:Q.44 Salt bridges: J:H.38 Metal complexes: J:H.38 BCL.26: 16 residues within 4Å: Chain J: H.25 Chain K: H.17, P.18, D.21, W.25 Chain L: H.20, W.23, K.24, V.27, V.31 Chain M: M.7 Ligands: QSE.23, BCL.24, QS2.27, BCL.29, QSE.30 4 PLIP interactions: 4 interactions with chain K, Hydrophobic interactions: K:P.18, K:W.25 pi-Stacking: K:H.17 Metal complexes: K:D.21 BCL.28: 21 residues within 4Å: Chain K: F.38, L.41, F.42, M.45, H.49, A.52, Y.58, F.60 Chain L: S.29, W.30, I.33, A.34, V.37, H.38, T.41 Chain M: I.48 Ligands: BCL.29, BCL.31, QS2.32, QSE.33, BCL.35 9 PLIP interactions: 7 interactions with chain K, 1 interactions with chain M, 1 interactions with chain L, Hydrophobic interactions: K:F.38, K:L.41, K:F.42, K:F.42, K:A.52, K:Y.58, M:I.48, L:V.37 Metal complexes: K:H.49 BCL.29: 20 residues within 4Å: Chain I: F.60 Chain K: L.41, Q.44, M.45, I.48, H.49, Y.58 Chain L: W.30, V.31, A.34, S.35, H.38, V.39, W.42, W.47, F.48 Ligands: BCL.24, BCL.26, BCL.28, QSE.30 15 PLIP interactions: 10 interactions with chain L, 3 interactions with chain K, 2 interactions with chain I, Hydrophobic interactions: L:W.30, L:W.30, L:A.34, L:H.38, L:W.42, L:W.47, L:W.47, L:F.48, K:I.48, K:Y.58, I:F.60, I:F.60 Salt bridges: L:H.38 Metal complexes: L:H.38 Hydrogen bonds: K:Q.44 BCL.31: 16 residues within 4Å: Chain A: M.7 Chain L: H.25 Chain M: H.17, P.18, D.21, W.25 Chain N: H.20, W.23, K.24, V.27, V.31 Ligands: BCL.28, QSE.30, QS2.32, QSE.33, BCL.35 3 PLIP interactions: 3 interactions with chain M, Hydrophobic interactions: M:P.18, M:W.25 Metal complexes: M:D.21 BCL.34: 21 residues within 4Å: Chain A: I.48 Chain M: F.38, L.41, F.42, M.45, H.49, A.52, Y.58, F.60 Chain N: S.29, W.30, I.33, A.34, V.37, H.38, T.41 Ligands: BCL.1, QS2.2, BCL.4, QSE.6, BCL.35 9 PLIP interactions: 7 interactions with chain M, 1 interactions with chain A, 1 interactions with chain N, Hydrophobic interactions: M:F.38, M:L.41, M:F.42, M:F.42, M:A.52, M:Y.58, A:I.48, N:V.37 Metal complexes: M:H.49 BCL.35: 21 residues within 4Å: Chain K: F.60 Chain M: L.41, Q.44, M.45, I.48, H.49, A.52, Y.58 Chain N: W.30, V.31, A.34, S.35, H.38, V.39, W.42, W.47, F.48 Ligands: BCL.28, BCL.31, QSE.33, BCL.34 16 PLIP interactions: 10 interactions with chain N, 4 interactions with chain M, 2 interactions with chain K, Hydrophobic interactions: N:W.30, N:W.30, N:A.34, N:H.38, N:W.42, N:W.47, N:W.47, N:F.48, M:I.48, M:A.52, M:Y.58, K:F.60, K:F.60 Salt bridges: N:H.38 Metal complexes: N:H.38 Hydrogen bonds: M:Q.44

7 x QS2: 9-cis-okenone(Non-covalent)

QS2.2: 14 residues within 4Å: Chain A: P.4, V.5, M.7, I.24, I.28, F.37 Chain B: W.23 Chain N: W.28, S.29, M.32, I.33 Ligands: BCL.1, QSE.6, BCL.34 9 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B, 3 interactions with chain N Hydrophobic interactions: A:P.4, A:V.5, A:V.5, A:F.37, A:F.37, B:W.23, N:M.32, N:I.33 pi-Stacking: N:W.28 QS2.5: 13 residues within 4Å: Chain B: W.28, S.29, M.32, I.33 Chain C: P.4, V.5, M.7, I.24, F.37 Chain D: W.23 Ligands: BCL.3, BCL.7, QSE.10 8 PLIP interactions: 3 interactions with chain B, 4 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: B:M.32, B:I.33, C:P.4, C:V.5, C:V.5, C:F.37, D:W.23 pi-Stacking: B:W.28 QS2.12: 14 residues within 4Å: Chain D: W.28, S.29, M.32, I.33 Chain E: P.4, V.5, M.7, I.24, I.28, F.37 Chain F: W.23 Ligands: BCL.8, BCL.11, QSE.13 8 PLIP interactions: 3 interactions with chain D, 1 interactions with chain F, 4 interactions with chain E Hydrophobic interactions: D:M.32, D:I.33, F:W.23, E:P.4, E:V.5, E:V.5, E:F.37 pi-Stacking: D:W.28 QS2.17: 14 residues within 4Å: Chain F: W.28, S.29, M.32, I.33 Chain G: P.4, V.5, M.7, I.24, I.28, F.37 Chain H: W.23 Ligands: BCL.14, BCL.16, QSE.18 8 PLIP interactions: 4 interactions with chain G, 3 interactions with chain F, 1 interactions with chain H Hydrophobic interactions: G:P.4, G:V.5, G:V.5, G:F.37, F:M.32, F:I.33, H:W.23 pi-Stacking: F:W.28 QS2.22: 14 residues within 4Å: Chain H: W.28, S.29, M.32, I.33 Chain I: P.4, V.5, M.7, I.24, I.28, F.37 Chain J: W.23 Ligands: BCL.19, BCL.21, QSE.23 8 PLIP interactions: 4 interactions with chain I, 1 interactions with chain J, 3 interactions with chain H Hydrophobic interactions: I:P.4, I:V.5, I:V.5, I:F.37, J:W.23, H:M.32, H:I.33 pi-Stacking: H:W.28 QS2.27: 14 residues within 4Å: Chain J: W.28, S.29, M.32, I.33 Chain K: P.4, V.5, M.7, I.24, I.28, F.37 Chain L: W.23 Ligands: BCL.24, BCL.26, QSE.30 8 PLIP interactions: 4 interactions with chain K, 3 interactions with chain J, 1 interactions with chain L Hydrophobic interactions: K:P.4, K:V.5, K:V.5, K:F.37, J:M.32, J:I.33, L:W.23 pi-Stacking: J:W.28 QS2.32: 14 residues within 4Å: Chain L: W.28, S.29, M.32, I.33 Chain M: P.4, V.5, M.7, I.24, I.28, F.37 Chain N: W.23 Ligands: BCL.28, BCL.31, QSE.33 8 PLIP interactions: 4 interactions with chain M, 1 interactions with chain N, 3 interactions with chain L Hydrophobic interactions: M:P.4, M:V.5, M:V.5, M:F.37, N:W.23, L:M.32, L:I.33 pi-Stacking: L:W.28

7 x QSE: all-trans okenone(Non-covalent)

QSE.6: 28 residues within 4Å: Chain A: M.34, F.37, F.38, L.41, Q.44, L.47, I.48, Y.51 Chain B: F.19, H.22, W.23, G.26, V.27, W.30 Chain C: H.17, K.23, I.24, V.27 Chain M: F.42, M.45, W.46, H.49, L.53 Ligands: BCL.1, QS2.2, BCL.4, BCL.7, BCL.34 18 PLIP interactions: 2 interactions with chain M, 3 interactions with chain C, 6 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: M:F.42, M:H.49, C:K.23, C:I.24, C:V.27, A:F.37, A:F.37, A:F.38, A:L.41, A:Y.51, B:F.19, B:H.22, B:W.23, B:V.27, B:W.30, B:W.30, B:W.30 Hydrogen bonds: A:Q.44 QSE.10: 28 residues within 4Å: Chain A: F.42, M.45, W.46, H.49, L.53 Chain C: M.34, F.37, F.38, L.41, Q.44, L.47, I.48, Y.51 Chain D: F.19, H.22, W.23, G.26, V.27, W.30 Chain E: H.17, K.23, I.24, V.27 Ligands: BCL.3, QS2.5, BCL.7, BCL.9, BCL.11 18 PLIP interactions: 2 interactions with chain A, 7 interactions with chain D, 6 interactions with chain C, 3 interactions with chain E Hydrophobic interactions: A:F.42, A:H.49, D:F.19, D:H.22, D:W.23, D:V.27, D:W.30, D:W.30, D:W.30, C:F.37, C:F.37, C:F.38, C:L.41, C:Y.51, E:K.23, E:I.24, E:V.27 Hydrogen bonds: C:Q.44 QSE.13: 28 residues within 4Å: Chain C: F.42, M.45, W.46, H.49, L.53 Chain E: M.34, F.37, F.38, L.41, Q.44, L.47, I.48, Y.51 Chain F: F.19, H.22, W.23, G.26, V.27, W.30 Chain G: H.17, K.23, I.24, V.27 Ligands: BCL.8, BCL.11, QS2.12, BCL.15, BCL.16 18 PLIP interactions: 3 interactions with chain G, 7 interactions with chain F, 6 interactions with chain E, 2 interactions with chain C Hydrophobic interactions: G:K.23, G:I.24, G:V.27, F:F.19, F:H.22, F:W.23, F:V.27, F:W.30, F:W.30, F:W.30, E:F.37, E:F.37, E:F.38, E:L.41, E:Y.51, C:F.42, C:H.49 Hydrogen bonds: E:Q.44 QSE.18: 28 residues within 4Å: Chain E: F.42, M.45, W.46, H.49, L.53 Chain G: M.34, F.37, F.38, L.41, Q.44, L.47, I.48, Y.51 Chain H: F.19, H.22, W.23, G.26, V.27, W.30 Chain I: H.17, K.23, I.24, V.27 Ligands: BCL.14, BCL.16, QS2.17, BCL.20, BCL.21 17 PLIP interactions: 7 interactions with chain H, 1 interactions with chain E, 6 interactions with chain G, 3 interactions with chain I Hydrophobic interactions: H:F.19, H:H.22, H:W.23, H:V.27, H:W.30, H:W.30, H:W.30, E:F.42, G:F.37, G:F.37, G:F.38, G:L.41, G:Y.51, I:K.23, I:I.24, I:V.27 Hydrogen bonds: G:Q.44 QSE.23: 28 residues within 4Å: Chain G: F.42, M.45, W.46, H.49, L.53 Chain I: M.34, F.37, F.38, L.41, Q.44, L.47, I.48, Y.51 Chain J: F.19, H.22, W.23, G.26, V.27, W.30 Chain K: H.17, K.23, I.24, V.27 Ligands: BCL.19, BCL.21, QS2.22, BCL.25, BCL.26 18 PLIP interactions: 2 interactions with chain G, 3 interactions with chain K, 7 interactions with chain J, 6 interactions with chain I Hydrophobic interactions: G:F.42, G:H.49, K:K.23, K:I.24, K:V.27, J:F.19, J:H.22, J:W.23, J:V.27, J:W.30, J:W.30, J:W.30, I:F.37, I:F.37, I:F.38, I:L.41, I:Y.51 Hydrogen bonds: I:Q.44 QSE.30: 27 residues within 4Å: Chain I: M.45, W.46, H.49, L.53 Chain K: M.34, F.37, F.38, L.41, Q.44, L.47, I.48, Y.51 Chain L: F.19, H.22, W.23, G.26, V.27, W.30 Chain M: H.17, K.23, I.24, V.27 Ligands: BCL.24, BCL.26, QS2.27, BCL.29, BCL.31 17 PLIP interactions: 6 interactions with chain K, 3 interactions with chain M, 7 interactions with chain L, 1 interactions with chain I Hydrophobic interactions: K:F.37, K:F.37, K:F.38, K:L.41, K:Y.51, M:K.23, M:I.24, M:V.27, L:F.19, L:H.22, L:W.23, L:V.27, L:W.30, L:W.30, L:W.30, I:H.49 Hydrogen bonds: K:Q.44 QSE.33: 27 residues within 4Å: Chain A: H.17, K.23, I.24, V.27 Chain K: M.45, W.46, H.49, L.53 Chain M: M.34, F.37, F.38, L.41, Q.44, L.47, I.48, Y.51 Chain N: F.19, H.22, W.23, G.26, V.27, W.30 Ligands: BCL.1, BCL.28, BCL.31, QS2.32, BCL.35 16 PLIP interactions: 7 interactions with chain N, 3 interactions with chain A, 6 interactions with chain M Hydrophobic interactions: N:F.19, N:H.22, N:W.23, N:V.27, N:W.30, N:W.30, N:W.30, A:K.23, A:I.24, A:V.27, M:F.37, M:F.37, M:F.38, M:L.41, M:Y.51 Hydrogen bonds: M:Q.44

Links

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Citation

Gardiner, A.T. et al., The 2.4 angstrom cryo-EM structure of a heptameric light-harvesting 2 complex reveals two carotenoid energy transfer pathways. Sci Adv (2021)

Release Date

2021-02-24

Peptides

LHC domain-containing protein: ACEGIKM
Light-harvesting protein B:800-850 subunit beta: BDFHJLN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

I
I

K
K

M
M

B
B

D
D

F
F

H
H

J
J

L
L

N
N

Membrane

We predict this structure to be a membrane protein.
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LHC domain-containing protein

Light-harvesting protein B:800-850 subunit beta