SMTL ID : 7y1a.1

Lateral hexamer

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-1-1-mer

Ligands

31 x PEB: PHYCOERYTHROBILIN(Covalent)

PEB.1: 18 residues within 4Å: Chain A: L.66, N.72, C.73, R.77, R.78, A.81, C.82, R.84, D.85, I.88, Y.117, L.120, V.122, S.126, S.127 Chain N: X.35, X.149, X.150 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.66, A:R.78, A:A.81, A:D.85, A:I.88, A:L.120 Hydrogen bonds: A:R.84, A:R.84, A:S.126 Salt bridges: A:R.77, A:R.78, A:R.84 pi-Cation interactions: A:R.84 PEB.2: 17 residues within 4Å: Chain A: A.32, N.35, K.36, L.38, D.39, N.42, I.142, T.143, N.144, F.153, A.154, A.155, G.156, D.157, C.158 Chain B: R.33, E.151 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:N.35, A:K.36, A:K.36, A:L.38, A:L.38, A:D.39, A:F.153, A:A.154 Hydrogen bonds: A:N.35, A:N.35, B:R.33 PEB.3: 12 residues within 4Å: Chain A: C.50, D.54, S.57, G.58, C.61, A.136, Q.137, F.141, T.145, A.146, T.147, R.149 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.141, A:F.141, A:T.147, A:R.149 Hydrogen bonds: A:Q.137 PEB.4: 15 residues within 4Å: Chain B: A.72, K.78, K.81, C.82, R.84, D.85, H.88, Y.89, L.120, L.122, P.123, A.126, Y.127 Chain G: Y.74, M.79 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:K.81, B:D.85, B:H.88, B:Y.89, B:L.120, B:L.122, B:L.122, B:A.126 Hydrogen bonds: B:R.84, B:D.85 Salt bridges: B:K.78, B:R.84 pi-Cation interactions: B:R.84 PEB.5: 8 residues within 4Å: Chain B: K.43, L.44, N.47, R.137, L.138, C.139, R.142, D.143 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.44, B:N.47, B:R.137 Hydrogen bonds: B:R.137, B:R.142 PEB.6: 16 residues within 4Å: Chain C: L.66, N.72, C.73, R.77, R.78, A.81, C.82, R.84, D.85, I.88, Y.117, L.120, V.122, S.126, S.127 Chain N: X.103 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:L.66, C:R.78, C:A.81, C:D.85, C:I.88, C:L.120 Hydrogen bonds: C:R.84, C:R.84, C:S.126 Salt bridges: C:R.77, C:R.78, C:R.84 pi-Cation interactions: C:R.84 PEB.7: 18 residues within 4Å: Chain B: L.24, Q.28 Chain C: A.32, N.35, K.36, L.38, D.39, N.42, I.142, T.143, N.144, F.153, A.154, A.155, G.156, D.157, C.158 Chain L: R.33 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:N.35, C:K.36, C:K.36, C:L.38, C:L.38, C:D.39, C:F.153, C:A.154, B:L.24 Hydrogen bonds: C:N.35, C:N.35 PEB.8: 12 residues within 4Å: Chain C: C.50, D.54, S.57, G.58, C.61, A.136, Q.137, F.141, T.145, A.146, T.147, R.149 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.141, C:F.141, C:T.147, C:R.149 Hydrogen bonds: C:Q.137 PEB.9: 15 residues within 4Å: Chain A: I.60, Y.74 Chain D: A.72, K.78, K.81, C.82, R.84, D.85, H.88, Y.89, L.120, L.122, P.123, A.126, Y.127 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:K.81, D:D.85, D:H.88, D:Y.89, D:L.120, D:L.122, D:L.122, D:A.126 Hydrogen bonds: D:R.84, D:D.85, D:H.88, D:Y.127 Salt bridges: D:K.78, D:R.84 pi-Cation interactions: D:R.84 PEB.10: 8 residues within 4Å: Chain D: K.43, L.44, N.47, R.137, L.138, C.139, R.142, D.143 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.44, D:N.47, D:R.137 Hydrogen bonds: D:R.137, D:R.142 PEB.11: 17 residues within 4Å: Chain E: L.66, N.72, C.73, R.77, R.78, A.81, C.82, R.84, D.85, I.88, Y.117, L.120, V.122, S.126, S.127 Chain N: X.48, X.51 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:L.66, E:R.78, E:A.81, E:D.85, E:I.88, E:L.120 Hydrogen bonds: E:R.84, E:R.84, E:S.126 Salt bridges: E:R.77, E:R.78, E:R.84 pi-Cation interactions: E:R.84 PEB.12: 17 residues within 4Å: Chain E: A.32, N.35, K.36, L.38, D.39, N.42, I.142, T.143, N.144, F.153, A.154, A.155, G.156, D.157, C.158 Chain F: R.33, E.151 11 PLIP interactions: 10 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:N.35, E:K.36, E:K.36, E:L.38, E:L.38, E:D.39, E:F.153, E:A.154, F:E.151 Hydrogen bonds: E:N.35, E:N.35 PEB.13: 12 residues within 4Å: Chain E: C.50, D.54, S.57, G.58, C.61, A.136, Q.137, F.141, T.145, A.146, T.147, R.149 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:F.141, E:F.141, E:T.147, E:R.149 Hydrogen bonds: E:Q.137, E:T.147 PEB.14: 17 residues within 4Å: Chain F: A.72, K.78, K.81, C.82, R.84, D.85, H.88, Y.89, L.120, L.122, P.123, A.126, Y.127 Chain K: S.57, I.60, I.67, Y.74 14 PLIP interactions: 13 interactions with chain F, 1 interactions with chain K Hydrophobic interactions: F:K.81, F:D.85, F:H.88, F:Y.89, F:L.120, F:L.122, F:L.122, F:A.126, K:I.67 Hydrogen bonds: F:R.84, F:D.85 Salt bridges: F:K.78, F:R.84 pi-Cation interactions: F:R.84 PEB.15: 8 residues within 4Å: Chain F: K.43, L.44, N.47, R.137, L.138, C.139, R.142, D.143 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:L.44, F:N.47, F:R.137 Hydrogen bonds: F:R.137, F:R.142 PEB.16: 17 residues within 4Å: Chain G: L.66, N.72, C.73, R.77, R.78, A.81, C.82, R.84, D.85, I.88, Y.117, L.120, V.122, S.126, S.127 Chain N: X.139, X.141 14 PLIP interactions: 14 interactions with chain G Hydrophobic interactions: G:L.66, G:R.78, G:A.81, G:D.85, G:I.88, G:L.120 Hydrogen bonds: G:R.84, G:R.84, G:Y.117, G:S.126 Salt bridges: G:R.77, G:R.78, G:R.84 pi-Cation interactions: G:R.84 PEB.17: 19 residues within 4Å: Chain D: R.33, V.150, E.151 Chain F: L.24 Chain G: A.32, N.35, K.36, L.38, D.39, N.42, I.142, T.143, N.144, F.153, A.154, A.155, G.156, D.157, C.158 13 PLIP interactions: 2 interactions with chain D, 10 interactions with chain G, 1 interactions with chain F Hydrophobic interactions: D:V.150, D:E.151, G:N.35, G:K.36, G:K.36, G:L.38, G:L.38, G:D.39, G:F.153, G:A.154, F:L.24 Hydrogen bonds: G:N.35, G:N.35 PEB.18: 12 residues within 4Å: Chain G: C.50, D.54, S.57, G.58, C.61, A.136, Q.137, F.141, T.145, A.146, T.147, R.149 5 PLIP interactions: 5 interactions with chain G Hydrophobic interactions: G:F.141, G:F.141, G:T.147, G:R.149 Hydrogen bonds: G:Q.137 PEB.19: 17 residues within 4Å: Chain E: S.57, I.60, Y.74, M.79 Chain H: A.72, K.78, K.81, C.82, R.84, D.85, H.88, Y.89, L.120, L.122, P.123, A.126, Y.127 15 PLIP interactions: 15 interactions with chain H Hydrophobic interactions: H:K.81, H:D.85, H:H.88, H:Y.89, H:L.120, H:L.122, H:L.122, H:A.126 Hydrogen bonds: H:R.84, H:D.85, H:H.88, H:Y.127 Salt bridges: H:K.78, H:R.84 pi-Cation interactions: H:R.84 PEB.20: 8 residues within 4Å: Chain H: K.43, L.44, N.47, R.137, L.138, C.139, R.142, D.143 5 PLIP interactions: 5 interactions with chain H Hydrophobic interactions: H:L.44, H:N.47, H:R.137 Hydrogen bonds: H:R.137, H:R.142 PEB.21: 17 residues within 4Å: Chain I: L.66, N.72, C.73, R.77, R.78, A.81, C.82, R.84, D.85, I.88, Y.117, L.120, V.122, S.126, S.127 Chain N: X.75, X.76 14 PLIP interactions: 14 interactions with chain I Hydrophobic interactions: I:L.66, I:R.78, I:A.81, I:D.85, I:I.88, I:L.120 Hydrogen bonds: I:R.84, I:R.84, I:Y.117, I:S.126 Salt bridges: I:R.77, I:R.78, I:R.84 pi-Cation interactions: I:R.84 PEB.22: 18 residues within 4Å: Chain H: L.24, Q.28 Chain I: A.32, N.35, K.36, L.38, D.39, N.42, I.142, T.143, N.144, F.153, A.154, A.155, G.156, D.157, C.158 Chain J: R.33 11 PLIP interactions: 10 interactions with chain I, 1 interactions with chain H Hydrophobic interactions: I:N.35, I:K.36, I:K.36, I:L.38, I:L.38, I:D.39, I:F.153, I:A.154, H:L.24 Hydrogen bonds: I:N.35, I:N.35 PEB.23: 12 residues within 4Å: Chain I: C.50, D.54, S.57, G.58, C.61, A.136, Q.137, F.141, T.145, A.146, T.147, R.149 6 PLIP interactions: 6 interactions with chain I Hydrophobic interactions: I:F.141, I:F.141, I:T.147, I:R.149 Hydrogen bonds: I:Q.137, I:T.147 PEB.24: 13 residues within 4Å: Chain J: A.72, K.78, K.81, C.82, R.84, D.85, H.88, Y.89, L.120, L.122, P.123, A.126, Y.127 12 PLIP interactions: 12 interactions with chain J Hydrophobic interactions: J:K.81, J:H.88, J:Y.89, J:L.120, J:L.122, J:L.122, J:A.126 Hydrogen bonds: J:R.84, J:D.85 Salt bridges: J:K.78, J:R.84 pi-Cation interactions: J:R.84 PEB.25: 8 residues within 4Å: Chain J: K.43, L.44, N.47, R.137, L.138, C.139, R.142, D.143 5 PLIP interactions: 5 interactions with chain J Hydrophobic interactions: J:L.44, J:N.47, J:R.137 Hydrogen bonds: J:R.137, J:R.142 PEB.26: 19 residues within 4Å: Chain K: L.66, N.72, C.73, R.77, R.78, A.81, C.82, R.84, D.85, I.88, Y.117, L.120, V.122, S.126, S.127 Chain N: X.113, X.116, X.117, X.120 14 PLIP interactions: 14 interactions with chain K Hydrophobic interactions: K:L.66, K:R.78, K:A.81, K:D.85, K:I.88, K:L.120 Hydrogen bonds: K:R.84, K:R.84, K:Y.117, K:S.126 Salt bridges: K:R.77, K:R.78, K:R.84 pi-Cation interactions: K:R.84 PEB.27: 18 residues within 4Å: Chain H: R.33 Chain J: L.24, Q.28 Chain K: A.32, N.35, K.36, L.38, D.39, N.42, I.142, T.143, N.144, F.153, A.154, A.155, G.156, D.157, C.158 11 PLIP interactions: 1 interactions with chain H, 10 interactions with chain K Hydrogen bonds: H:R.33, K:N.35, K:N.35 Hydrophobic interactions: K:N.35, K:K.36, K:K.36, K:L.38, K:L.38, K:D.39, K:F.153, K:A.154 PEB.28: 12 residues within 4Å: Chain K: C.50, D.54, S.57, G.58, C.61, A.136, Q.137, F.141, T.145, A.146, T.147, R.149 5 PLIP interactions: 5 interactions with chain K Hydrophobic interactions: K:F.141, K:F.141, K:T.147, K:R.149 Hydrogen bonds: K:Q.137 PEB.29: 6 residues within 4Å: Chain J: E.42, A.45, G.46 Chain K: Y.18, G.21, S.22 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:Y.18 PEB.30: 15 residues within 4Å: Chain I: Y.74, M.79 Chain L: A.72, K.78, K.81, C.82, R.84, D.85, H.88, Y.89, L.120, L.122, P.123, A.126, Y.127 15 PLIP interactions: 15 interactions with chain L Hydrophobic interactions: L:K.81, L:D.85, L:H.88, L:Y.89, L:L.120, L:L.122, L:L.122, L:A.126 Hydrogen bonds: L:R.84, L:D.85, L:H.88, L:Y.127 Salt bridges: L:K.78, L:R.84 pi-Cation interactions: L:R.84 PEB.31: 8 residues within 4Å: Chain L: K.43, L.44, N.47, R.137, L.138, C.139, R.142, D.143 5 PLIP interactions: 5 interactions with chain L Hydrophobic interactions: L:L.44, L:N.47, L:R.137 Hydrogen bonds: L:R.137, L:R.142

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

You, X. et al., In situ structure of the red algal phycobilisome-PSII-PSI-LHC megacomplex. Nature (2023)

Release Date

2023-01-18

Peptides

B-phycoerythrin beta chain: ACEGIK
Phycoerythrin alpha subunit: BDFHJL
LRH: M
LRH: N

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
y

C
1

E
q

G
s

I
u

K
w

B
z

D
p

F
r

H
t

J
v

L
x

M
a

N
A

B-phycoerythrin beta chain

Phycoerythrin alpha subunit

LRH

LRH

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