SMTL ID : 7tv3.1

LH2-LH3 antenna in parallel configuration embedded in a nanodisc

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-8-8-8-8-mer

Ligands

48 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)(Non-functional Binders)

BCL.1: 3 residues within 4Å: Chain A: N.3, P.4 Ligands: LYC.6 1 PLIP interactions: 1 interactions with chain A, Hydrophobic interactions: A:N.3 BCL.2: 2 residues within 4Å: Ligands: BCL.4, BCL.11 0 PLIP interactions: BCL.4: 4 residues within 4Å: Chain B: A.32 Ligands: BCL.2, LYC.3, BCL.23 1 PLIP interactions: 1 interactions with chain B, Hydrophobic interactions: B:A.32 BCL.5: 3 residues within 4Å: Chain C: N.3, P.4 Ligands: LYC.25 1 PLIP interactions: 1 interactions with chain C, Hydrophobic interactions: C:N.3 BCL.7: 2 residues within 4Å: Ligands: BCL.12, BCL.16 0 PLIP interactions: BCL.9: 3 residues within 4Å: Chain D: N.3, P.4 Ligands: LYC.13 1 PLIP interactions: 1 interactions with chain D, Hydrophobic interactions: D:N.3 BCL.10: 2 residues within 4Å: Ligands: BCL.11, BCL.12 0 PLIP interactions: BCL.11: 4 residues within 4Å: Chain E: A.32 Ligands: BCL.2, LYC.8, BCL.10 1 PLIP interactions: 1 interactions with chain E, Hydrophobic interactions: E:A.32 BCL.12: 4 residues within 4Å: Chain F: A.32 Ligands: LYC.6, BCL.7, BCL.10 1 PLIP interactions: 1 interactions with chain F, Hydrophobic interactions: F:A.32 BCL.14: 3 residues within 4Å: Chain G: N.3, P.4 Ligands: LYC.29 1 PLIP interactions: 1 interactions with chain G, Hydrophobic interactions: G:N.3 BCL.15: 2 residues within 4Å: Ligands: BCL.16, BCL.28 0 PLIP interactions: BCL.16: 4 residues within 4Å: Chain H: A.32 Ligands: BCL.7, LYC.13, BCL.15 1 PLIP interactions: 1 interactions with chain H, Hydrophobic interactions: H:A.32 BCL.17: 3 residues within 4Å: Chain I: N.3, P.4 Ligands: LYC.3 1 PLIP interactions: 1 interactions with chain I, Hydrophobic interactions: I:N.3 BCL.18: 2 residues within 4Å: Ligands: BCL.20, BCL.24 0 PLIP interactions: BCL.20: 4 residues within 4Å: Chain J: A.32 Ligands: BCL.18, LYC.19, BCL.31 1 PLIP interactions: 1 interactions with chain J, Hydrophobic interactions: J:A.32 BCL.22: 3 residues within 4Å: Chain K: N.3, P.4 Ligands: LYC.8 1 PLIP interactions: 1 interactions with chain K, Hydrophobic interactions: K:N.3 BCL.23: 2 residues within 4Å: Ligands: BCL.4, BCL.24 0 PLIP interactions: BCL.24: 4 residues within 4Å: Chain L: A.32 Ligands: BCL.18, LYC.21, BCL.23 1 PLIP interactions: 1 interactions with chain L, Hydrophobic interactions: L:A.32 BCL.26: 3 residues within 4Å: Chain M: N.3, P.4 Ligands: LYC.19 1 PLIP interactions: 1 interactions with chain M, Hydrophobic interactions: M:N.3 BCL.27: 2 residues within 4Å: Ligands: BCL.28, BCL.32 0 PLIP interactions: BCL.28: 4 residues within 4Å: Chain N: A.32 Ligands: BCL.15, LYC.25, BCL.27 1 PLIP interactions: 1 interactions with chain N, Hydrophobic interactions: N:A.32 BCL.30: 3 residues within 4Å: Chain O: N.3, P.4 Ligands: LYC.21 1 PLIP interactions: 1 interactions with chain O, Hydrophobic interactions: O:N.3 BCL.31: 2 residues within 4Å: Ligands: BCL.20, BCL.32 0 PLIP interactions: BCL.32: 4 residues within 4Å: Chain P: A.32 Ligands: BCL.27, LYC.29, BCL.31 1 PLIP interactions: 1 interactions with chain P, Hydrophobic interactions: P:A.32 BCL.33: 3 residues within 4Å: Chain Q: N.3, P.4 Ligands: LYC.41 1 PLIP interactions: 1 interactions with chain Q, Hydrophobic interactions: Q:N.3 BCL.34: 2 residues within 4Å: Ligands: BCL.36, BCL.40 0 PLIP interactions: BCL.36: 4 residues within 4Å: Chain R: A.35 Ligands: BCL.34, LYC.35, BCL.55 1 PLIP interactions: 1 interactions with chain R, Hydrophobic interactions: R:A.35 BCL.38: 3 residues within 4Å: Chain S: N.3, P.4 Ligands: LYC.45 1 PLIP interactions: 1 interactions with chain S, Hydrophobic interactions: S:N.3 BCL.39: 2 residues within 4Å: Ligands: BCL.40, BCL.44 0 PLIP interactions: BCL.40: 4 residues within 4Å: Chain T: A.35 Ligands: BCL.34, LYC.37, BCL.39 1 PLIP interactions: 1 interactions with chain T, Hydrophobic interactions: T:A.35 BCL.42: 3 residues within 4Å: Chain U: N.3, P.4 Ligands: LYC.57 1 PLIP interactions: 1 interactions with chain U, Hydrophobic interactions: U:N.3 BCL.43: 2 residues within 4Å: Ligands: BCL.44, BCL.48 0 PLIP interactions: BCL.44: 4 residues within 4Å: Chain V: A.35 Ligands: BCL.39, LYC.41, BCL.43 1 PLIP interactions: 1 interactions with chain V, Hydrophobic interactions: V:A.35 BCL.46: 3 residues within 4Å: Chain W: N.3, P.4 Ligands: LYC.61 1 PLIP interactions: 1 interactions with chain W, Hydrophobic interactions: W:N.3 BCL.47: 2 residues within 4Å: Ligands: BCL.48, BCL.60 0 PLIP interactions: BCL.48: 4 residues within 4Å: Chain X: A.35 Ligands: BCL.43, LYC.45, BCL.47 1 PLIP interactions: 1 interactions with chain X, Hydrophobic interactions: X:A.35 BCL.49: 3 residues within 4Å: Chain Y: N.3, P.4 Ligands: LYC.35 1 PLIP interactions: 1 interactions with chain Y, Hydrophobic interactions: Y:N.3 BCL.50: 2 residues within 4Å: Ligands: BCL.52, BCL.56 0 PLIP interactions: BCL.52: 4 residues within 4Å: Chain Z: A.35 Ligands: BCL.50, LYC.51, BCL.63 1 PLIP interactions: 1 interactions with chain Z, Hydrophobic interactions: Z:A.35 BCL.54: 3 residues within 4Å: Chain 0: N.3, P.4 Ligands: LYC.37 1 PLIP interactions: 1 interactions with chain 0, Hydrophobic interactions: 0:N.3 BCL.55: 2 residues within 4Å: Ligands: BCL.36, BCL.56 0 PLIP interactions: BCL.56: 4 residues within 4Å: Chain 1: A.35 Ligands: BCL.50, LYC.53, BCL.55 1 PLIP interactions: 1 interactions with chain 1, Hydrophobic interactions: 1:A.35 BCL.58: 3 residues within 4Å: Chain 2: N.3, P.4 Ligands: LYC.51 1 PLIP interactions: 1 interactions with chain 2, Hydrophobic interactions: 2:N.3 BCL.59: 2 residues within 4Å: Ligands: BCL.60, BCL.64 0 PLIP interactions: BCL.60: 4 residues within 4Å: Chain 3: A.35 Ligands: BCL.47, LYC.57, BCL.59 1 PLIP interactions: 1 interactions with chain 3, Hydrophobic interactions: 3:A.35 BCL.62: 3 residues within 4Å: Chain 4: N.3, P.4 Ligands: LYC.53 1 PLIP interactions: 1 interactions with chain 4, Hydrophobic interactions: 4:N.3 BCL.63: 2 residues within 4Å: Ligands: BCL.52, BCL.64 0 PLIP interactions: BCL.64: 4 residues within 4Å: Chain 5: A.35 Ligands: BCL.59, LYC.61, BCL.63 1 PLIP interactions: 1 interactions with chain 5, Hydrophobic interactions: 5:A.35

16 x LYC: LYCOPENE(Non-covalent)

LYC.3: 14 residues within 4Å: Chain A: A.31, I.32, H.35 Chain I: K.9, I.10, L.12 Chain K: A.27 Chain L: A.13, V.14, Q.17, F.18, T.21 Ligands: BCL.4, BCL.17 8 PLIP interactions: 3 interactions with chain L, 2 interactions with chain I, 1 interactions with chain K, 2 interactions with chain A Hydrophobic interactions: L:A.13, L:Q.17, L:T.21, I:K.9, I:L.12, K:A.27, A:A.31, A:H.35 LYC.6: 14 residues within 4Å: Chain A: K.9, I.10, L.12 Chain C: A.31, I.32, H.35 Chain D: A.27 Chain E: A.13, V.14, Q.17, F.18, T.21 Ligands: BCL.1, BCL.12 8 PLIP interactions: 3 interactions with chain E, 2 interactions with chain A, 2 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: E:A.13, E:Q.17, E:T.21, A:K.9, A:L.12, C:A.31, C:H.35, D:A.27 LYC.8: 12 residues within 4Å: Chain A: A.27 Chain B: A.13, V.14, Q.17, F.18, T.21 Chain D: A.31, I.32, H.35 Chain K: L.12 Ligands: BCL.11, BCL.22 7 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B, 2 interactions with chain D, 1 interactions with chain K Hydrophobic interactions: A:A.27, B:A.13, B:Q.17, B:T.21, D:A.31, D:H.35, K:L.12 LYC.13: 12 residues within 4Å: Chain C: A.27 Chain D: L.12 Chain F: A.13, V.14, Q.17, F.18, T.21 Chain G: A.31, I.32, H.35 Ligands: BCL.9, BCL.16 7 PLIP interactions: 1 interactions with chain C, 2 interactions with chain G, 3 interactions with chain F, 1 interactions with chain D Hydrophobic interactions: C:A.27, G:A.31, G:H.35, F:A.13, F:Q.17, F:T.21, D:L.12 LYC.19: 14 residues within 4Å: Chain I: A.31, I.32, H.35 Chain M: K.9, I.10, L.12 Chain O: A.27 Chain P: A.13, V.14, Q.17, F.18, T.21 Ligands: BCL.20, BCL.26 8 PLIP interactions: 2 interactions with chain M, 3 interactions with chain P, 2 interactions with chain I, 1 interactions with chain O Hydrophobic interactions: M:K.9, M:L.12, P:A.13, P:Q.17, P:T.21, I:A.31, I:H.35, O:A.27 LYC.21: 12 residues within 4Å: Chain I: A.27 Chain J: A.13, V.14, Q.17, F.18, T.21 Chain K: A.31, I.32, H.35 Chain O: L.12 Ligands: BCL.24, BCL.30 7 PLIP interactions: 2 interactions with chain K, 1 interactions with chain I, 3 interactions with chain J, 1 interactions with chain O Hydrophobic interactions: K:A.31, K:H.35, I:A.27, J:A.13, J:Q.17, J:T.21, O:L.12 LYC.25: 14 residues within 4Å: Chain C: K.9, I.10, L.12 Chain G: A.27 Chain H: A.13, V.14, Q.17, F.18, T.21 Chain M: A.31, I.32, H.35 Ligands: BCL.5, BCL.28 8 PLIP interactions: 2 interactions with chain C, 3 interactions with chain H, 2 interactions with chain M, 1 interactions with chain G Hydrophobic interactions: C:K.9, C:L.12, H:A.13, H:Q.17, H:T.21, M:A.31, M:H.35, G:A.27 LYC.29: 12 residues within 4Å: Chain G: L.12 Chain M: A.27 Chain N: A.13, V.14, Q.17, F.18, T.21 Chain O: A.31, I.32, H.35 Ligands: BCL.14, BCL.32 7 PLIP interactions: 1 interactions with chain G, 3 interactions with chain N, 2 interactions with chain O, 1 interactions with chain M Hydrophobic interactions: G:L.12, N:A.13, N:Q.17, N:T.21, O:A.31, O:H.35, M:A.27 LYC.35: 15 residues within 4Å: Chain 0: A.27, F.37 Chain 1: A.16, V.17, Q.20, F.21, T.24 Chain Q: A.31, I.32, H.35 Chain Y: K.9, I.10, L.12 Ligands: BCL.36, BCL.49 9 PLIP interactions: 2 interactions with chain Y, 2 interactions with chain Q, 2 interactions with chain 0, 3 interactions with chain 1 Hydrophobic interactions: Y:K.9, Y:L.12, Q:A.31, Q:H.35, 0:A.27, 0:F.37, 1:A.16, 1:Q.20, 1:T.24 LYC.37: 13 residues within 4Å: Chain 0: L.12 Chain Q: A.27, F.37 Chain R: A.16, V.17, Q.20, F.21, T.24 Chain S: A.31, I.32, H.35 Ligands: BCL.40, BCL.54 8 PLIP interactions: 2 interactions with chain Q, 3 interactions with chain R, 2 interactions with chain S, 1 interactions with chain 0 Hydrophobic interactions: Q:A.27, Q:F.37, R:A.16, R:Q.20, R:T.24, S:A.31, S:H.35, 0:L.12 LYC.41: 15 residues within 4Å: Chain Q: K.9, I.10, L.12 Chain S: A.27, F.37 Chain T: A.16, V.17, Q.20, F.21, T.24 Chain U: A.31, I.32, H.35 Ligands: BCL.33, BCL.44 9 PLIP interactions: 2 interactions with chain Q, 2 interactions with chain U, 3 interactions with chain T, 2 interactions with chain S Hydrophobic interactions: Q:K.9, Q:L.12, U:A.31, U:H.35, T:A.16, T:Q.20, T:T.24, S:A.27, S:F.37 LYC.45: 13 residues within 4Å: Chain S: L.12 Chain U: A.27, F.37 Chain V: A.16, V.17, Q.20, F.21, T.24 Chain W: A.31, I.32, H.35 Ligands: BCL.38, BCL.48 8 PLIP interactions: 2 interactions with chain W, 2 interactions with chain U, 3 interactions with chain V, 1 interactions with chain S Hydrophobic interactions: W:A.31, W:H.35, U:A.27, U:F.37, V:A.16, V:Q.20, V:T.24, S:L.12 LYC.51: 15 residues within 4Å: Chain 2: K.9, I.10, L.12 Chain 4: A.27, F.37 Chain 5: A.16, V.17, Q.20, F.21, T.24 Chain Y: A.31, I.32, H.35 Ligands: BCL.52, BCL.58 9 PLIP interactions: 3 interactions with chain 5, 2 interactions with chain 4, 2 interactions with chain Y, 2 interactions with chain 2 Hydrophobic interactions: 5:A.16, 5:Q.20, 5:T.24, 4:A.27, 4:F.37, Y:A.31, Y:H.35, 2:K.9, 2:L.12 LYC.53: 13 residues within 4Å: Chain 0: A.31, I.32, H.35 Chain 4: L.12 Chain Y: A.27, F.37 Chain Z: A.16, V.17, Q.20, F.21, T.24 Ligands: BCL.56, BCL.62 8 PLIP interactions: 3 interactions with chain Z, 2 interactions with chain 0, 2 interactions with chain Y, 1 interactions with chain 4 Hydrophobic interactions: Z:A.16, Z:Q.20, Z:T.24, 0:A.31, 0:H.35, Y:A.27, Y:F.37, 4:L.12 LYC.57: 15 residues within 4Å: Chain 2: A.31, I.32, H.35 Chain U: K.9, I.10, L.12 Chain W: A.27, F.37 Chain X: A.16, V.17, Q.20, F.21, T.24 Ligands: BCL.42, BCL.60 9 PLIP interactions: 3 interactions with chain X, 2 interactions with chain 2, 2 interactions with chain W, 2 interactions with chain U Hydrophobic interactions: X:A.16, X:Q.20, X:T.24, 2:A.31, 2:H.35, W:A.27, W:F.37, U:K.9, U:L.12 LYC.61: 13 residues within 4Å: Chain 2: A.27, F.37 Chain 3: A.16, V.17, Q.20, F.21, T.24 Chain 4: A.31, I.32, H.35 Chain W: L.12 Ligands: BCL.46, BCL.64 8 PLIP interactions: 3 interactions with chain 3, 1 interactions with chain W, 2 interactions with chain 2, 2 interactions with chain 4 Hydrophobic interactions: 3:A.16, 3:Q.20, 3:T.24, W:L.12, 2:A.27, 2:F.37, 4:A.31, 4:H.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, D. et al., Elucidating interprotein energy transfer dynamics within the antenna network from purple bacteria. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2023-02-15

Peptides

Light-harvesting protein B-800/850 alpha chain: ACDGIKMO
Light-harvesting protein B-800/850 beta 1 chain: BEFHJLNP
Light-harvesting protein B800-820 alpha chain: QSUWY024
Light-harvesting protein B800-820 beta chain: RTVXZ135

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

D
D

G
G

I
I

K
K

M
M

O
O

B
B

E
E

F
F

H
H

J
J

L
L

N
N

P
P

Q
Q

S
S

U
U

W
W

Y
Y

0
a

2
c

4
e

R
R

T
T

V
V

X
X

Z
Z

1
b

3
d

5
f

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 1 chain

Light-harvesting protein B800-820 alpha chain

Light-harvesting protein B800-820 beta chain

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