SMTL ID : 8fb9.1

LH2-LH3 antenna in anti 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.2, P.3 Ligands: LYC.17 1 PLIP interactions: 1 interactions with chain A, Hydrophobic interactions: A:N.2 BCL.2: 2 residues within 4Å: Ligands: BCL.4, BCL.8 0 PLIP interactions: BCL.4: 4 residues within 4Å: Chain B: A.34 Ligands: BCL.2, LYC.3, BCL.31 1 PLIP interactions: 1 interactions with chain B, Hydrophobic interactions: B:A.34 BCL.6: 3 residues within 4Å: Chain C: N.2, P.3 Ligands: LYC.21 1 PLIP interactions: 1 interactions with chain C, Hydrophobic interactions: C:N.2 BCL.7: 2 residues within 4Å: Ligands: BCL.8, BCL.20 0 PLIP interactions: BCL.8: 4 residues within 4Å: Chain D: A.34 Ligands: BCL.2, LYC.5, BCL.7 1 PLIP interactions: 1 interactions with chain D, Hydrophobic interactions: D:A.34 BCL.9: 3 residues within 4Å: Chain E: N.2, P.3 Ligands: LYC.25 1 PLIP interactions: 1 interactions with chain E, Hydrophobic interactions: E:N.2 BCL.10: 2 residues within 4Å: Ligands: BCL.12, BCL.16 0 PLIP interactions: BCL.12: 4 residues within 4Å: Chain F: A.34 Ligands: BCL.10, LYC.11, BCL.23 1 PLIP interactions: 1 interactions with chain F, Hydrophobic interactions: F:A.34 BCL.14: 3 residues within 4Å: Chain G: N.2, P.3 Ligands: LYC.29 1 PLIP interactions: 1 interactions with chain G, Hydrophobic interactions: G:N.2 BCL.15: 2 residues within 4Å: Ligands: BCL.16, BCL.28 0 PLIP interactions: BCL.16: 4 residues within 4Å: Chain H: A.34 Ligands: BCL.10, LYC.13, BCL.15 1 PLIP interactions: 1 interactions with chain H, Hydrophobic interactions: H:A.34 BCL.18: 3 residues within 4Å: Chain I: N.2, P.3 Ligands: LYC.11 1 PLIP interactions: 1 interactions with chain I, Hydrophobic interactions: I:N.2 BCL.19: 2 residues within 4Å: Ligands: BCL.20, BCL.24 0 PLIP interactions: BCL.20: 4 residues within 4Å: Chain J: A.34 Ligands: BCL.7, LYC.17, BCL.19 1 PLIP interactions: 1 interactions with chain J, Hydrophobic interactions: J:A.34 BCL.22: 3 residues within 4Å: Chain K: N.2, P.3 Ligands: LYC.13 1 PLIP interactions: 1 interactions with chain K, Hydrophobic interactions: K:N.2 BCL.23: 2 residues within 4Å: Ligands: BCL.12, BCL.24 0 PLIP interactions: BCL.24: 4 residues within 4Å: Chain L: A.34 Ligands: BCL.19, LYC.21, BCL.23 1 PLIP interactions: 1 interactions with chain L, Hydrophobic interactions: L:A.34 BCL.26: 3 residues within 4Å: Chain M: N.2, P.3 Ligands: LYC.3 1 PLIP interactions: 1 interactions with chain M, Hydrophobic interactions: M:N.2 BCL.27: 2 residues within 4Å: Ligands: BCL.28, BCL.32 0 PLIP interactions: BCL.28: 4 residues within 4Å: Chain N: A.34 Ligands: BCL.15, LYC.25, BCL.27 1 PLIP interactions: 1 interactions with chain N, Hydrophobic interactions: N:A.34 BCL.30: 3 residues within 4Å: Chain O: N.2, P.3 Ligands: LYC.5 1 PLIP interactions: 1 interactions with chain O, Hydrophobic interactions: O:N.2 BCL.31: 2 residues within 4Å: Ligands: BCL.4, BCL.32 0 PLIP interactions: BCL.32: 4 residues within 4Å: Chain P: A.34 Ligands: BCL.27, LYC.29, BCL.31 1 PLIP interactions: 1 interactions with chain P, Hydrophobic interactions: P:A.34 BCL.33: 3 residues within 4Å: Chain Q: N.2, P.3 Ligands: LYC.41 1 PLIP interactions: 1 interactions with chain Q, Hydrophobic interactions: Q:N.2 BCL.34: 2 residues within 4Å: Ligands: BCL.36, BCL.40 0 PLIP interactions: BCL.36: 4 residues within 4Å: Chain R: A.34 Ligands: BCL.34, LYC.35, BCL.63 1 PLIP interactions: 1 interactions with chain R, Hydrophobic interactions: R:A.34 BCL.38: 3 residues within 4Å: Chain S: N.2, P.3 Ligands: LYC.45 1 PLIP interactions: 1 interactions with chain S, Hydrophobic interactions: S:N.2 BCL.39: 2 residues within 4Å: Ligands: BCL.40, BCL.44 0 PLIP interactions: BCL.40: 4 residues within 4Å: Chain T: A.34 Ligands: BCL.34, LYC.37, BCL.39 1 PLIP interactions: 1 interactions with chain T, Hydrophobic interactions: T:A.34 BCL.42: 3 residues within 4Å: Chain U: N.2, P.3 Ligands: LYC.49 1 PLIP interactions: 1 interactions with chain U, Hydrophobic interactions: U:N.2 BCL.43: 2 residues within 4Å: Ligands: BCL.44, BCL.48 0 PLIP interactions: BCL.44: 4 residues within 4Å: Chain V: A.34 Ligands: BCL.39, LYC.41, BCL.43 1 PLIP interactions: 1 interactions with chain V, Hydrophobic interactions: V:A.34 BCL.46: 3 residues within 4Å: Chain W: N.2, P.3 Ligands: LYC.53 1 PLIP interactions: 1 interactions with chain W, Hydrophobic interactions: W:N.2 BCL.47: 2 residues within 4Å: Ligands: BCL.48, BCL.52 0 PLIP interactions: BCL.48: 4 residues within 4Å: Chain X: A.34 Ligands: BCL.43, LYC.45, BCL.47 1 PLIP interactions: 1 interactions with chain X, Hydrophobic interactions: X:A.34 BCL.50: 3 residues within 4Å: Chain Y: N.2, P.3 Ligands: LYC.57 1 PLIP interactions: 1 interactions with chain Y, Hydrophobic interactions: Y:N.2 BCL.51: 2 residues within 4Å: Ligands: BCL.52, BCL.56 0 PLIP interactions: BCL.52: 4 residues within 4Å: Chain Z: A.34 Ligands: BCL.47, LYC.49, BCL.51 1 PLIP interactions: 1 interactions with chain Z, Hydrophobic interactions: Z:A.34 BCL.54: 3 residues within 4Å: Chain 0: N.2, P.3 Ligands: LYC.61 1 PLIP interactions: 1 interactions with chain 0, Hydrophobic interactions: 0:N.2 BCL.55: 2 residues within 4Å: Ligands: BCL.56, BCL.60 0 PLIP interactions: BCL.56: 4 residues within 4Å: Chain 1: A.34 Ligands: BCL.51, LYC.53, BCL.55 1 PLIP interactions: 1 interactions with chain 1, Hydrophobic interactions: 1:A.34 BCL.58: 3 residues within 4Å: Chain 2: N.2, P.3 Ligands: LYC.35 1 PLIP interactions: 1 interactions with chain 2, Hydrophobic interactions: 2:N.2 BCL.59: 2 residues within 4Å: Ligands: BCL.60, BCL.64 0 PLIP interactions: BCL.60: 4 residues within 4Å: Chain 3: A.34 Ligands: BCL.55, LYC.57, BCL.59 1 PLIP interactions: 1 interactions with chain 3, Hydrophobic interactions: 3:A.34 BCL.62: 3 residues within 4Å: Chain 4: N.2, P.3 Ligands: LYC.37 1 PLIP interactions: 1 interactions with chain 4, Hydrophobic interactions: 4:N.2 BCL.63: 2 residues within 4Å: Ligands: BCL.36, BCL.64 0 PLIP interactions: BCL.64: 4 residues within 4Å: Chain 5: A.34 Ligands: BCL.59, LYC.61, BCL.63 1 PLIP interactions: 1 interactions with chain 5, Hydrophobic interactions: 5:A.34

16 x LYC: LYCOPENE(Non-covalent)

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

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

2023-07-19

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
D

E
C

G
G

I
I

K
K

M
c

O
e

B
B

D
E

F
F

H
H

J
J

L
L

N
d

P
f

Q
M

S
O

U
Q

W
S

Y
U

0
W

2
Y

4
a

R
N

T
P

V
R

X
T

Z
V

1
X

3
Z

5
b

Membrane

We predict this structure to be a membrane protein.
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Light-harvesting protein B800-820 alpha chain

Light-harvesting protein B800-820 beta chain

Light-harvesting protein B-800/850 alpha chain

Light-harvesting protein B-800/850 beta 1 chain

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