SMTL ID : 8jc8.1

Cryo-EM structure of the LH1 complex from thermochromatium tepidum

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-15-15-mer

Ligands

30 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.1: 16 residues within 4Å: Chain 1: Q.28, L.31, G.32, I.35, H.36 Chain A: F.30, V.33, V.34, H.37, W.41, W.46 Chain B: L.47 Ligands: BCL.3, CRT.5, 8K6.7, BCL.70 11 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B, 3 interactions with chain 1, Hydrophobic interactions: A:F.30, A:V.33, A:V.34, A:W.41, A:W.46, A:W.46, B:L.47, 1:I.35, 1:I.35 Metal complexes: A:H.37 Hydrogen bonds: 1:Q.28 BCL.3: 13 residues within 4Å: Chain 1: I.35 Chain B: Q.28, I.29, H.36, W.46 Chain C: W.29, V.33, A.36, H.37 Ligands: BCL.1, CRT.5, BCL.6, 8K6.7 8 PLIP interactions: 5 interactions with chain B, 2 interactions with chain 1, 1 interactions with chain C, Hydrophobic interactions: B:Q.28, B:I.29, B:W.46, B:W.46, 1:I.35, 1:I.35, C:W.29 Metal complexes: B:H.36 BCL.6: 16 residues within 4Å: Chain B: Q.28, L.31, G.32, I.35, H.36 Chain C: F.30, V.33, V.34, H.37, W.41, W.46 Chain D: L.47 Ligands: BCL.3, CRT.8, BCL.9, 8K6.11 13 PLIP interactions: 10 interactions with chain C, 2 interactions with chain B, 1 interactions with chain D, Hydrophobic interactions: C:F.30, C:V.33, C:V.34, C:W.41, C:W.41, C:W.46, C:W.46, C:W.46, C:W.46, B:I.35, D:L.47 Metal complexes: C:H.37 Hydrogen bonds: B:Q.28 BCL.9: 15 residues within 4Å: Chain B: I.35 Chain D: Q.28, I.29, G.32, H.36, W.46 Chain E: W.29, V.33, A.36, H.37, A.40 Ligands: BCL.6, CRT.8, 8K6.11, BCL.12 9 PLIP interactions: 5 interactions with chain D, 3 interactions with chain E, 1 interactions with chain B, Hydrophobic interactions: D:Q.28, D:I.29, D:W.46, D:W.46, E:W.29, E:W.29, E:A.40, B:I.35 Metal complexes: D:H.36 BCL.12: 17 residues within 4Å: Chain D: Q.28, L.31, G.32, I.35, H.36 Chain E: W.29, F.30, V.33, V.34, H.37, W.41, W.46 Chain F: L.47 Ligands: BCL.9, CRT.13, BCL.14, 8K6.17 12 PLIP interactions: 9 interactions with chain E, 2 interactions with chain D, 1 interactions with chain F, Hydrophobic interactions: E:F.30, E:V.33, E:V.34, E:W.41, E:W.46, E:W.46, E:W.46, E:W.46, D:I.35, F:L.47 Metal complexes: E:H.37 Hydrogen bonds: D:Q.28 BCL.14: 18 residues within 4Å: Chain D: I.11, L.15, I.35 Chain F: V.25, Q.28, I.29, H.36, W.46 Chain G: W.29, V.33, A.36, H.37, A.40 Ligands: BCL.12, CRT.13, BCL.16, 8K6.17, CRT.19 12 PLIP interactions: 7 interactions with chain F, 3 interactions with chain D, 2 interactions with chain G, Hydrophobic interactions: F:V.25, F:V.25, F:Q.28, F:I.29, F:W.46, F:W.46, D:I.11, D:L.15, D:I.35, G:W.29, G:A.40 Metal complexes: F:H.36 BCL.16: 17 residues within 4Å: Chain F: Q.28, L.31, G.32, I.35, H.36 Chain G: W.29, F.30, V.33, V.34, H.37, W.41, W.46 Chain H: L.47 Ligands: BCL.14, 8K6.18, CRT.19, BCL.20 12 PLIP interactions: 2 interactions with chain F, 9 interactions with chain G, 1 interactions with chain H, Hydrophobic interactions: F:I.35, G:F.30, G:V.34, G:H.37, G:W.41, G:W.46, G:W.46, G:W.46, G:W.46, H:L.47 Hydrogen bonds: F:Q.28 Metal complexes: G:H.37 BCL.20: 13 residues within 4Å: Chain F: I.35 Chain H: Q.28, I.29, G.32, H.36, W.46 Chain I: W.29, A.36, H.37 Ligands: BCL.16, 8K6.18, CRT.19, BCL.22 7 PLIP interactions: 5 interactions with chain H, 1 interactions with chain F, 1 interactions with chain I, Hydrophobic interactions: H:Q.28, H:I.29, H:W.46, H:W.46, F:I.35, I:W.29 Metal complexes: H:H.36 BCL.22: 18 residues within 4Å: Chain H: Q.28, L.31, G.32, I.35, H.36 Chain I: W.29, F.30, V.33, V.34, H.37, W.41, W.46, L.47 Chain J: L.47 Ligands: BCL.20, CRT.23, BCL.24, 8K6.27 11 PLIP interactions: 9 interactions with chain I, 1 interactions with chain H, 1 interactions with chain J, Hydrophobic interactions: I:F.30, I:V.33, I:V.34, I:W.41, I:W.46, I:W.46, I:W.46, I:L.47, H:I.35, J:L.47 Metal complexes: I:H.37 BCL.24: 14 residues within 4Å: Chain J: Q.28, I.29, G.32, H.36, W.46 Chain K: W.29, V.33, A.36, H.37, A.40 Ligands: BCL.22, CRT.23, 8K6.27, BCL.28 8 PLIP interactions: 2 interactions with chain K, 6 interactions with chain J, Hydrophobic interactions: K:W.29, K:A.40, J:Q.28, J:I.29, J:W.46, J:W.46 pi-Stacking: J:H.36 Metal complexes: J:H.36 BCL.28: 16 residues within 4Å: Chain J: Q.28, L.31, G.32, I.35, H.36 Chain K: F.30, V.33, H.37, W.41, W.46, L.47 Chain L: L.47 Ligands: BCL.24, CRT.26, BCL.29, 8K6.31 11 PLIP interactions: 8 interactions with chain K, 1 interactions with chain L, 2 interactions with chain J, Hydrophobic interactions: K:F.30, K:V.33, K:W.41, K:W.46, K:W.46, K:W.46, K:L.47, L:L.47, J:I.35 Metal complexes: K:H.37 Hydrogen bonds: J:Q.28 BCL.29: 13 residues within 4Å: Chain L: Q.28, I.29, G.32, H.36, W.46 Chain M: W.29, V.33, A.36, H.37 Ligands: CRT.26, BCL.28, 8K6.31, BCL.32 6 PLIP interactions: 5 interactions with chain L, 1 interactions with chain M, Hydrophobic interactions: L:Q.28, L:I.29, L:W.46, L:W.46, M:W.29 Metal complexes: L:H.36 BCL.32: 18 residues within 4Å: Chain L: Q.28, L.31, G.32, I.35, H.36 Chain M: W.29, F.30, V.33, V.34, H.37, W.41, W.46, L.47 Chain N: L.47 Ligands: BCL.29, CRT.33, BCL.34, 8K6.37 11 PLIP interactions: 8 interactions with chain M, 1 interactions with chain N, 2 interactions with chain L, Hydrophobic interactions: M:F.30, M:V.34, M:W.41, M:W.41, M:W.46, M:W.46, M:L.47, N:L.47, L:I.35, L:I.35 Metal complexes: M:H.37 BCL.34: 14 residues within 4Å: Chain L: I.35 Chain N: Q.28, I.29, G.32, H.36, W.46 Chain O: W.29, A.36, H.37, A.40 Ligands: BCL.32, CRT.33, 8K6.37, BCL.38 8 PLIP interactions: 5 interactions with chain N, 1 interactions with chain L, 2 interactions with chain O, Hydrophobic interactions: N:Q.28, N:I.29, N:W.46, N:W.46, L:I.35, O:W.29, O:A.40 Metal complexes: N:H.36 BCL.38: 16 residues within 4Å: Chain N: Q.28, L.31, G.32, I.35, H.36 Chain O: F.30, V.33, V.34, H.37, W.41, W.46 Chain P: L.47 Ligands: BCL.34, CRT.36, 8K6.39, BCL.40 13 PLIP interactions: 9 interactions with chain O, 3 interactions with chain N, 1 interactions with chain P, Hydrophobic interactions: O:F.30, O:V.33, O:V.33, O:V.34, O:W.41, O:W.46, O:W.46, O:W.46, N:I.35, N:I.35, P:L.47 Metal complexes: O:H.37 Hydrogen bonds: N:Q.28 BCL.40: 15 residues within 4Å: Chain N: I.35 Chain P: Q.28, I.29, G.32, H.36, W.46 Chain Q: W.29, V.33, A.36, H.37, A.40 Ligands: CRT.36, BCL.38, 8K6.39, BCL.44 8 PLIP interactions: 2 interactions with chain Q, 5 interactions with chain P, 1 interactions with chain N, Hydrophobic interactions: Q:W.29, Q:A.40, P:Q.28, P:I.29, P:W.46, P:W.46, N:I.35 Metal complexes: P:H.36 BCL.44: 18 residues within 4Å: Chain P: Q.28, L.31, G.32, I.35, H.36 Chain Q: W.29, F.30, V.33, V.34, H.37, W.41, W.46, L.47 Chain R: L.47 Ligands: BCL.40, CRT.43, BCL.45, 8K6.48 12 PLIP interactions: 9 interactions with chain Q, 2 interactions with chain P, 1 interactions with chain R, Hydrophobic interactions: Q:F.30, Q:V.33, Q:V.34, Q:W.41, Q:W.41, Q:W.46, Q:W.46, Q:L.47, P:I.35, R:L.47 Metal complexes: Q:H.37 Hydrogen bonds: P:Q.28 BCL.45: 14 residues within 4Å: Chain P: I.35 Chain R: Q.28, I.29, G.32, H.36, W.46 Chain S: W.29, A.36, H.37, A.40 Ligands: CRT.43, BCL.44, BCL.47, 8K6.48 9 PLIP interactions: 6 interactions with chain R, 1 interactions with chain P, 2 interactions with chain S, Hydrophobic interactions: R:Q.28, R:I.29, R:W.46, R:W.46, P:I.35, S:W.29, S:A.40 pi-Stacking: R:H.36 Metal complexes: R:H.36 BCL.47: 19 residues within 4Å: Chain R: Q.28, L.31, G.32, I.35, H.36, V.39 Chain S: W.29, F.30, V.33, V.34, H.37, W.41, W.46, L.47 Chain T: L.47 Ligands: CRT.42, BCL.45, BCL.49, 8K6.52 12 PLIP interactions: 3 interactions with chain R, 8 interactions with chain S, 1 interactions with chain T, Hydrophobic interactions: R:I.35, R:V.39, S:V.33, S:V.34, S:W.41, S:W.46, S:W.46, S:W.46, S:L.47, T:L.47 Hydrogen bonds: R:Q.28 Metal complexes: S:H.37 BCL.49: 15 residues within 4Å: Chain R: I.35 Chain T: Q.28, I.29, H.36, W.46 Chain U: W.29, L.32, V.33, A.36, H.37 Ligands: CRT.42, BCL.47, BCL.51, 8K6.52, CRT.53 9 PLIP interactions: 5 interactions with chain T, 1 interactions with chain R, 3 interactions with chain U, Hydrophobic interactions: T:Q.28, T:I.29, T:W.46, T:W.46, R:I.35, U:W.29, U:W.29, U:W.29 Metal complexes: T:H.36 BCL.51: 17 residues within 4Å: Chain T: Q.28, L.31, G.32, I.35, H.36 Chain U: W.29, F.30, V.33, V.34, H.37, W.41, W.46 Chain V: L.47 Ligands: BCL.49, CRT.53, BCL.54, 8K6.57 12 PLIP interactions: 9 interactions with chain U, 2 interactions with chain T, 1 interactions with chain V, Hydrophobic interactions: U:F.30, U:V.33, U:V.33, U:V.34, U:W.41, U:W.41, U:W.46, U:W.46, T:I.35, V:L.47 Metal complexes: U:H.37 Hydrogen bonds: T:Q.28 BCL.54: 13 residues within 4Å: Chain V: Q.28, I.29, H.36, W.46 Chain W: W.29, V.33, A.36, H.37, A.40 Ligands: BCL.51, CRT.53, BCL.56, 8K6.57 7 PLIP interactions: 5 interactions with chain V, 2 interactions with chain W, Hydrophobic interactions: V:Q.28, V:I.29, V:W.46, W:W.29, W:A.40 pi-Stacking: V:H.36 Metal complexes: V:H.36 BCL.56: 17 residues within 4Å: Chain V: Q.28, L.31, G.32, I.35, H.36 Chain W: W.29, F.30, V.33, V.34, H.37, W.41, W.46 Chain X: L.47 Ligands: BCL.54, CRT.58, BCL.59, 8K6.63 12 PLIP interactions: 9 interactions with chain W, 2 interactions with chain V, 1 interactions with chain X, Hydrophobic interactions: W:F.30, W:V.33, W:V.34, W:W.41, W:W.41, W:W.46, W:W.46, W:W.46, V:I.35, X:L.47 Metal complexes: W:H.37 Hydrogen bonds: V:Q.28 BCL.59: 14 residues within 4Å: Chain X: Q.28, I.29, G.32, H.36, W.46 Chain Y: W.29, V.33, A.36, H.37, A.40 Ligands: BCL.56, CRT.58, BCL.61, 8K6.63 7 PLIP interactions: 2 interactions with chain Y, 5 interactions with chain X, Hydrophobic interactions: Y:W.29, Y:A.40, X:Q.28, X:I.29, X:W.46, X:W.46 Metal complexes: X:H.36 BCL.61: 17 residues within 4Å: Chain X: Q.28, L.31, G.32, I.35, H.36 Chain Y: F.30, V.33, V.34, H.37, W.41, W.46, L.47 Chain Z: L.47 Ligands: BCL.59, CRT.62, BCL.64, 8K6.74 13 PLIP interactions: 10 interactions with chain Y, 2 interactions with chain X, 1 interactions with chain Z, Hydrophobic interactions: Y:F.30, Y:V.33, Y:V.34, Y:H.37, Y:W.41, Y:W.41, Y:W.46, Y:W.46, Y:L.47, X:I.35, Z:L.47 Metal complexes: Y:H.37 Hydrogen bonds: X:Q.28 BCL.64: 13 residues within 4Å: Chain 3: W.29, A.36, H.37, A.40 Chain X: I.35 Chain Z: Q.28, G.32, H.36, W.46 Ligands: BCL.61, CRT.62, 8K6.74, BCL.75 7 PLIP interactions: 1 interactions with chain X, 4 interactions with chain Z, 2 interactions with chain 3, Hydrophobic interactions: X:I.35, Z:Q.28, Z:W.46, Z:W.46, 3:W.29, 3:A.40 Metal complexes: Z:H.36 BCL.66: 17 residues within 4Å: Chain 0: W.29, F.30, V.33, H.37, W.41, W.46, L.47 Chain 1: L.47 Chain 2: Q.28, L.31, G.32, I.35, H.36 Ligands: 8K6.2, CRT.69, BCL.70, BCL.73 14 PLIP interactions: 10 interactions with chain 0, 3 interactions with chain 2, 1 interactions with chain 1, Hydrophobic interactions: 0:F.30, 0:V.33, 0:H.37, 0:W.41, 0:W.41, 0:W.46, 0:W.46, 0:W.46, 0:L.47, 2:I.35, 2:I.35, 1:L.47 Metal complexes: 0:H.37 Hydrogen bonds: 2:Q.28 BCL.70: 15 residues within 4Å: Chain 1: Q.28, I.29, G.32, H.36, W.46 Chain 2: I.35 Chain A: W.29, V.33, A.36, H.37, A.40 Ligands: BCL.1, 8K6.2, BCL.66, CRT.69 8 PLIP interactions: 4 interactions with chain 1, 2 interactions with chain A, 2 interactions with chain 2, Hydrophobic interactions: 1:Q.28, 1:I.29, 1:W.46, 1:W.46, A:W.29, A:A.40, 2:I.35, 2:I.35 BCL.73: 13 residues within 4Å: Chain 0: W.29, A.36, H.37, A.40 Chain 2: Q.28, I.29, G.32, H.36, W.46 Ligands: BCL.66, 8K6.67, CRT.71, BCL.75 7 PLIP interactions: 2 interactions with chain 0, 5 interactions with chain 2, Hydrophobic interactions: 0:W.29, 0:A.40, 2:Q.28, 2:I.29, 2:W.46, 2:W.46 Metal complexes: 2:H.36 BCL.75: 16 residues within 4Å: Chain 2: L.47 Chain 3: F.30, V.33, H.37, W.41, W.46, L.47 Chain Z: Q.28, L.31, G.32, I.35, H.36 Ligands: BCL.64, 8K6.67, CRT.71, BCL.73 13 PLIP interactions: 10 interactions with chain 3, 2 interactions with chain Z, 1 interactions with chain 2, Hydrophobic interactions: 3:F.30, 3:V.33, 3:H.37, 3:W.41, 3:W.46, 3:W.46, 3:W.46, 3:W.46, 3:L.47, Z:I.35, 2:L.47 Metal complexes: 3:H.37 Hydrogen bonds: Z:Q.28

15 x 8K6: Octadecane(Non-covalent)

8K6.2: 3 residues within 4Å: Chain A: Y.43 Ligands: BCL.66, BCL.70 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.43 8K6.7: 5 residues within 4Å: Chain C: A.36, A.40, Y.43 Ligands: BCL.1, BCL.3 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:A.36, C:Y.43 8K6.11: 3 residues within 4Å: Chain C: L.47 Ligands: BCL.6, BCL.9 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.47 8K6.17: 5 residues within 4Å: Chain E: L.47 Chain G: A.36, Y.43 Ligands: BCL.12, BCL.14 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:A.36, G:Y.43 8K6.18: 5 residues within 4Å: Chain G: L.47 Chain I: A.36, Y.43 Ligands: BCL.16, BCL.20 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain I Hydrophobic interactions: G:L.47, I:A.36 8K6.27: 5 residues within 4Å: Chain K: A.36, A.40, Y.43 Ligands: BCL.22, BCL.24 2 PLIP interactions: 2 interactions with chain K Hydrophobic interactions: K:A.36, K:Y.43 8K6.31: 5 residues within 4Å: Chain K: L.47 Chain M: L.39, Y.43 Ligands: BCL.28, BCL.29 4 PLIP interactions: 1 interactions with chain K, 3 interactions with chain M Hydrophobic interactions: K:L.47, M:L.39, M:L.39, M:Y.43 8K6.37: 7 residues within 4Å: Chain M: L.47 Chain O: A.36, L.39, L.42, Y.43 Ligands: BCL.32, BCL.34 5 PLIP interactions: 1 interactions with chain M, 4 interactions with chain O Hydrophobic interactions: M:L.47, O:A.36, O:L.42, O:Y.43, O:Y.43 8K6.39: 6 residues within 4Å: Chain O: L.47 Chain Q: A.36, L.39, Y.43 Ligands: BCL.38, BCL.40 4 PLIP interactions: 3 interactions with chain Q, 1 interactions with chain O Hydrophobic interactions: Q:A.36, Q:L.39, Q:Y.43, O:L.47 8K6.48: 5 residues within 4Å: Chain Q: L.47 Chain S: A.36, Y.43 Ligands: BCL.44, BCL.45 2 PLIP interactions: 1 interactions with chain S, 1 interactions with chain Q Hydrophobic interactions: S:A.36, Q:L.47 8K6.52: 7 residues within 4Å: Chain S: L.47 Chain U: A.36, L.39, A.40, Y.43 Ligands: BCL.47, BCL.49 2 PLIP interactions: 1 interactions with chain U, 1 interactions with chain S Hydrophobic interactions: U:L.39, S:L.47 8K6.57: 6 residues within 4Å: Chain U: L.47 Chain W: A.36, L.42, Y.43 Ligands: BCL.51, BCL.54 4 PLIP interactions: 1 interactions with chain U, 3 interactions with chain W Hydrophobic interactions: U:L.47, W:A.36, W:Y.43, W:Y.43 8K6.63: 4 residues within 4Å: Chain W: L.47 Chain Y: Y.43 Ligands: BCL.56, BCL.59 2 PLIP interactions: 1 interactions with chain Y, 1 interactions with chain W Hydrophobic interactions: Y:Y.43, W:L.47 8K6.67: 5 residues within 4Å: Chain 0: A.36, Y.43 Chain 3: L.47 Ligands: BCL.73, BCL.75 4 PLIP interactions: 1 interactions with chain 3, 3 interactions with chain 0 Hydrophobic interactions: 3:L.47, 0:A.36, 0:Y.43, 0:Y.43 8K6.74: 4 residues within 4Å: Chain 3: L.42 Chain Y: L.47 Ligands: BCL.61, BCL.64 No protein-ligand interaction detected (PLIP)

15 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain A: W.46 Chain B: W.46, D.49, I.51 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Metal complexes: B:W.46, B:D.49, B:I.51, A:W.46 CA.10: 4 residues within 4Å: Chain C: W.46 Chain D: W.46, D.49, I.51 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Metal complexes: C:W.46, D:W.46, D:D.49, D:I.51 CA.15: 4 residues within 4Å: Chain E: W.46 Chain F: W.46, D.49, I.51 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain E Metal complexes: F:W.46, F:D.49, F:I.51, E:W.46 CA.21: 4 residues within 4Å: Chain G: W.46 Chain H: W.46, D.49, I.51 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain G Metal complexes: H:W.46, H:D.49, H:I.51, G:W.46 CA.25: 4 residues within 4Å: Chain I: W.46 Chain J: W.46, D.49, I.51 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain I Metal complexes: J:W.46, J:D.49, J:I.51, I:W.46 CA.30: 4 residues within 4Å: Chain K: W.46 Chain L: W.46, D.49, I.51 4 PLIP interactions: 3 interactions with chain L, 1 interactions with chain K Metal complexes: L:W.46, L:D.49, L:I.51, K:W.46 CA.35: 4 residues within 4Å: Chain M: W.46 Chain N: W.46, D.49, I.51 4 PLIP interactions: 3 interactions with chain N, 1 interactions with chain M Metal complexes: N:W.46, N:D.49, N:I.51, M:W.46 CA.41: 4 residues within 4Å: Chain O: W.46 Chain P: W.46, D.49, I.51 4 PLIP interactions: 1 interactions with chain O, 3 interactions with chain P Metal complexes: O:W.46, P:W.46, P:D.49, P:I.51 CA.46: 4 residues within 4Å: Chain Q: W.46 Chain R: W.46, D.49, I.51 4 PLIP interactions: 3 interactions with chain R, 1 interactions with chain Q Metal complexes: R:W.46, R:D.49, R:I.51, Q:W.46 CA.50: 4 residues within 4Å: Chain S: W.46 Chain T: W.46, D.49, I.51 4 PLIP interactions: 3 interactions with chain T, 1 interactions with chain S Metal complexes: T:W.46, T:D.49, T:I.51, S:W.46 CA.55: 4 residues within 4Å: Chain U: W.46 Chain V: W.46, D.49, I.51 4 PLIP interactions: 3 interactions with chain V, 1 interactions with chain U Metal complexes: V:W.46, V:D.49, V:I.51, U:W.46 CA.60: 4 residues within 4Å: Chain W: W.46 Chain X: W.46, D.49, I.51 4 PLIP interactions: 3 interactions with chain X, 1 interactions with chain W Metal complexes: X:W.46, X:D.49, X:I.51, W:W.46 CA.65: 4 residues within 4Å: Chain Y: W.46 Chain Z: W.46, D.49, I.51 5 PLIP interactions: 1 interactions with chain Y, 4 interactions with chain Z Metal complexes: Y:W.46, Z:W.46, Z:D.49, Z:D.49, Z:I.51 CA.68: 4 residues within 4Å: Chain 0: W.46 Chain 1: W.46, D.49, I.51 4 PLIP interactions: 1 interactions with chain 0, 3 interactions with chain 1 Metal complexes: 0:W.46, 1:W.46, 1:D.49, 1:I.51 CA.72: 4 residues within 4Å: Chain 2: W.46, D.49, I.51 Chain 3: W.46 4 PLIP interactions: 3 interactions with chain 2, 1 interactions with chain 3 Metal complexes: 2:W.46, 2:D.49, 2:I.51, 3:W.46

15 x CRT: SPIRILLOXANTHIN(Non-covalent)

CRT.5: 24 residues within 4Å: Chain 1: L.21, I.24, F.27, Q.28, L.34, I.35, I.38 Chain 2: N.7, L.8, K.10, I.11, I.14 Chain A: E.17, F.18, I.21, F.22, S.25, M.26, F.30 Chain B: L.33, H.36, M.37 Ligands: BCL.1, BCL.3 13 PLIP interactions: 6 interactions with chain A, 3 interactions with chain 2, 4 interactions with chain 1 Hydrophobic interactions: A:F.18, A:F.18, A:I.21, A:F.22, A:F.22, A:F.30, 2:K.10, 2:I.11, 2:I.11, 1:L.21, 1:I.24, 1:F.27, 1:I.35 CRT.8: 21 residues within 4Å: Chain 1: L.8, K.10, I.11, I.14 Chain B: L.21, F.27, Q.28, L.34, I.35, I.38 Chain C: E.17, F.18, I.21, F.22, S.25, M.26 Chain D: L.33, H.36, M.37 Ligands: BCL.6, BCL.9 12 PLIP interactions: 7 interactions with chain C, 3 interactions with chain B, 2 interactions with chain 1 Hydrophobic interactions: C:E.17, C:F.18, C:F.18, C:I.21, C:I.21, C:F.22, C:F.22, B:L.21, B:F.27, B:I.35, 1:I.11, 1:I.11 CRT.13: 22 residues within 4Å: Chain B: N.7, L.8, K.10, I.11 Chain D: L.21, F.27, Q.28, L.34, I.35, I.38 Chain E: E.17, F.18, I.21, F.22, S.25, M.26, F.30 Chain F: L.33, H.36, M.37 Ligands: BCL.12, BCL.14 12 PLIP interactions: 7 interactions with chain E, 3 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: E:F.18, E:F.18, E:I.21, E:I.21, E:F.22, E:F.22, E:F.30, D:L.21, D:F.27, D:I.35, B:I.11, B:I.11 CRT.19: 22 residues within 4Å: Chain D: N.7, L.8, K.10, I.11, I.14 Chain F: L.21, F.27, Q.28, I.35, I.38 Chain G: E.17, F.18, I.21, F.22, S.25, M.26 Chain H: L.33, H.36, M.37 Ligands: BCL.14, BCL.16, BCL.20 14 PLIP interactions: 3 interactions with chain F, 7 interactions with chain G, 2 interactions with chain H, 2 interactions with chain D Hydrophobic interactions: F:L.21, F:F.27, F:I.35, G:F.18, G:F.18, G:I.21, G:I.21, G:F.22, G:F.22, G:F.22, H:L.33, H:H.36, D:I.11, D:I.11 CRT.23: 20 residues within 4Å: Chain F: L.8, K.10, I.11, I.14 Chain H: F.27, Q.28, L.34, I.35, I.38 Chain I: E.17, F.18, I.21, F.22, S.25, M.26 Chain J: L.33, H.36, M.37 Ligands: BCL.22, BCL.24 10 PLIP interactions: 7 interactions with chain I, 1 interactions with chain F, 2 interactions with chain H Hydrophobic interactions: I:F.18, I:F.18, I:I.21, I:I.21, I:F.22, I:F.22, I:F.22, F:I.11, H:F.27, H:I.35 CRT.26: 22 residues within 4Å: Chain H: N.7, L.8, K.10, I.11, I.14 Chain J: L.21, F.27, Q.28, L.34, I.35, I.38 Chain K: E.14, F.18, I.21, F.22, S.25, M.26 Chain L: L.33, H.36, M.37 Ligands: BCL.28, BCL.29 13 PLIP interactions: 3 interactions with chain H, 7 interactions with chain K, 3 interactions with chain J Hydrophobic interactions: H:K.10, H:I.11, H:I.14, K:E.14, K:F.18, K:F.18, K:I.21, K:I.21, K:F.22, K:F.22, J:L.21, J:F.27, J:I.35 CRT.33: 21 residues within 4Å: Chain J: L.8, K.10, I.11, I.14 Chain L: L.21, F.27, Q.28, L.34, I.35, I.38 Chain M: E.17, F.18, I.21, F.22, S.25, M.26 Chain N: L.33, H.36, M.37 Ligands: BCL.32, BCL.34 14 PLIP interactions: 7 interactions with chain M, 3 interactions with chain L, 4 interactions with chain J Hydrophobic interactions: M:F.18, M:F.18, M:I.21, M:I.21, M:F.22, M:F.22, M:F.22, L:L.21, L:F.27, L:I.35, J:K.10, J:I.11, J:I.11, J:I.14 CRT.36: 19 residues within 4Å: Chain L: N.7, L.8, K.10, I.11, I.14 Chain N: F.27, Q.28, I.35, I.38 Chain O: F.18, I.21, F.22, S.25, M.26 Chain P: L.33, H.36, M.37 Ligands: BCL.38, BCL.40 12 PLIP interactions: 7 interactions with chain O, 2 interactions with chain L, 2 interactions with chain N, 1 interactions with chain P Hydrophobic interactions: O:F.18, O:F.18, O:I.21, O:I.21, O:F.22, O:F.22, O:F.22, L:L.8, L:K.10, N:F.27, N:I.35, P:H.36 CRT.42: 19 residues within 4Å: Chain P: L.8, K.10, I.11, I.14 Chain R: L.21, F.27, Q.28, I.35, I.38 Chain S: F.18, I.21, F.22, S.25, M.26 Chain T: L.33, H.36, M.37 Ligands: BCL.47, BCL.49 13 PLIP interactions: 3 interactions with chain R, 2 interactions with chain P, 7 interactions with chain S, 1 interactions with chain T Hydrophobic interactions: R:L.21, R:F.27, R:I.35, P:I.11, P:I.11, S:F.18, S:F.18, S:I.21, S:I.21, S:F.22, S:F.22, S:F.22, T:H.36 CRT.43: 19 residues within 4Å: Chain N: N.7, L.8, K.10, I.11, I.14 Chain P: L.21, F.27, I.35, I.38 Chain Q: F.18, I.21, F.22, S.25, M.26 Chain R: L.33, H.36, M.37 Ligands: BCL.44, BCL.45 13 PLIP interactions: 7 interactions with chain Q, 1 interactions with chain R, 3 interactions with chain P, 2 interactions with chain N Hydrophobic interactions: Q:F.18, Q:F.18, Q:I.21, Q:I.21, Q:F.22, Q:F.22, Q:F.22, R:H.36, P:L.21, P:F.27, P:I.35, N:K.10, N:I.11 CRT.53: 21 residues within 4Å: Chain R: L.8, K.10, I.11 Chain T: L.21, F.27, Q.28, L.34, I.35, I.38 Chain U: E.14, F.18, I.21, F.22, S.25, M.26 Chain V: L.33, H.36, M.37 Ligands: BCL.49, BCL.51, BCL.54 12 PLIP interactions: 3 interactions with chain T, 7 interactions with chain U, 2 interactions with chain R Hydrophobic interactions: T:L.21, T:F.27, T:I.35, U:E.14, U:F.18, U:F.18, U:I.21, U:I.21, U:F.22, U:F.22, R:I.11, R:I.11 CRT.58: 23 residues within 4Å: Chain T: N.7, L.8, K.10, I.11, I.14 Chain V: L.21, F.27, Q.28, L.34, I.35, I.38 Chain W: E.14, E.17, F.18, I.21, F.22, S.25, M.26 Chain X: L.33, H.36, M.37 Ligands: BCL.56, BCL.59 14 PLIP interactions: 8 interactions with chain W, 3 interactions with chain V, 2 interactions with chain T, 1 interactions with chain X Hydrophobic interactions: W:E.14, W:F.18, W:F.18, W:I.21, W:I.21, W:F.22, W:F.22, W:F.22, V:L.21, V:F.27, V:I.35, T:K.10, T:I.11, X:L.33 CRT.62: 21 residues within 4Å: Chain V: N.7, L.8, K.10, I.11 Chain X: L.21, F.27, Q.28, I.35, I.38 Chain Y: E.14, E.17, F.18, I.21, F.22, S.25, M.26 Chain Z: L.33, H.36, M.37 Ligands: BCL.61, BCL.64 14 PLIP interactions: 3 interactions with chain X, 8 interactions with chain Y, 2 interactions with chain V, 1 interactions with chain Z Hydrophobic interactions: X:L.21, X:F.27, X:I.35, Y:E.14, Y:F.18, Y:F.18, Y:I.21, Y:I.21, Y:F.22, Y:F.22, Y:F.22, V:K.10, V:I.11, Z:H.36 CRT.69: 14 residues within 4Å: Chain 0: F.22 Chain 1: L.33, H.36, M.37 Chain 2: I.24, F.27, Q.28, L.34, I.35, I.38 Chain Z: K.10, I.11 Ligands: BCL.66, BCL.70 7 PLIP interactions: 1 interactions with chain Z, 2 interactions with chain 1, 3 interactions with chain 2, 1 interactions with chain 0 Hydrophobic interactions: Z:K.10, 1:L.33, 1:H.36, 2:I.24, 2:F.27, 2:I.35, 0:F.22 CRT.71: 21 residues within 4Å: Chain 2: L.33, H.36, M.37 Chain 3: E.14, E.17, F.18, I.21, F.22, S.25 Chain X: L.8, K.10, I.11, I.14 Chain Z: L.21, F.27, Q.28, L.34, I.35, I.38 Ligands: BCL.73, BCL.75 13 PLIP interactions: 1 interactions with chain 2, 3 interactions with chain Z, 7 interactions with chain 3, 2 interactions with chain X Hydrophobic interactions: 2:H.36, Z:L.21, Z:F.27, Z:I.35, 3:E.14, 3:F.18, 3:F.18, 3:I.21, 3:I.21, 3:F.22, 3:F.22, X:I.11, X:I.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yan, Y.H. et al., Molecular structure and characterization of the Thermochromatium tepidum light-harvesting 1 photocomplex produced in a foreign host. Biochim Biophys Acta Bioenerg (2024)

Release Date

2024-11-13

Peptides

LH1 beta polypeptide: ACEGIKMOQSUWY03
LH1 alpha polypeptide: BDFHJLNPRTVXZ12

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
2

C
4

E
6

G
8

I
B

K
E

M
G

O
J

Q
N

S
P

U
R

W
T

Y
V

0
Z

3
X

B
3

D
5

F
7

H
A

J
D

L
F

N
I

P
K

R
O

T
Q

V
S

X
U

Z
W

1
1

2
Y

Membrane

We predict this structure to be a membrane protein.
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LH1 beta polypeptide

LH1 alpha polypeptide

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