SMTL ID : 9v7k.1

Phycobilisome allophycocyanin hexamer C from Gloeobacter violaceus PCC 7421

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-6-6-1-1-mer

Ligands

12 x CYC: PHYCOCYANOBILIN(Covalent)

CYC.1: 24 residues within 4Å: Chain C: L.58, V.65, N.71, M.77, L.80, C.81, R.83, D.84, Y.87, Y.88, I.107, M.115, Y.116, L.119, T.121, P.122, A.125 Chain J: I.61, Y.62, T.66, Y.73, T.74, T.75, Y.78 21 PLIP interactions: 13 interactions with chain C, 8 interactions with chain J Hydrophobic interactions: C:L.58, C:L.80, C:Y.87, C:Y.88, C:I.107, C:L.119, C:A.125, J:I.61, J:Y.62, J:T.75, J:Y.78 Hydrogen bonds: C:N.71, C:R.83, C:D.84, C:T.121, J:Y.62, J:T.66, J:T.74 Salt bridges: C:R.83, J:K.53 pi-Cation interactions: C:R.83 CYC.2: 25 residues within 4Å: Chain A: F.1008, L.1135, I.1136, S.1139 Chain D: L.60, N.71, M.72, R.77, A.80, C.81, R.83, D.84, M.85, Y.87, F.88, R.107, V.108, L.112, T.115, Y.116, L.119, V.121, P.122, A.125, T.126 19 PLIP interactions: 14 interactions with chain D, 5 interactions with chain A Hydrophobic interactions: D:L.60, D:L.60, D:A.80, D:Y.87, D:F.88, D:L.112, D:T.115, D:Y.116, D:L.119, D:V.121, D:A.125, A:F.1008, A:F.1008, A:F.1008, A:F.1008, A:I.1136 Hydrogen bonds: D:R.83, D:D.84 Salt bridges: D:R.83 CYC.3: 23 residues within 4Å: Chain E: V.65, N.71, A.72, M.77, L.80, C.81, R.83, D.84, Y.87, Y.88, I.107, M.115, Y.116, L.119, T.121, P.122 Chain N: I.61, Y.62, T.66, Y.73, T.74, T.75, Y.78 19 PLIP interactions: 10 interactions with chain E, 9 interactions with chain N Hydrophobic interactions: E:L.80, E:L.80, E:Y.87, E:Y.88, E:T.121, N:I.61, N:Y.62, N:Y.73, N:T.75, N:Y.78 Hydrogen bonds: E:N.71, E:N.71, E:R.83, E:D.84, N:Y.62, N:Y.62, N:T.74 Salt bridges: E:R.83, N:K.53 CYC.4: 24 residues within 4Å: Chain F: L.65, N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, M.85, Y.87, F.88, V.108, L.112, Y.116, L.119, V.121, P.122, A.125, T.126 Chain O: R.21, E.22, L.23, T.26 19 PLIP interactions: 15 interactions with chain F, 4 interactions with chain O Hydrophobic interactions: F:A.80, F:Y.87, F:F.88, F:V.108, F:L.112, F:Y.116, F:L.119, F:V.121, F:V.121, F:A.125, O:L.23, O:L.23 Hydrogen bonds: F:R.83, F:R.83, F:D.84, O:E.22, O:L.23 Salt bridges: F:R.76, F:R.83 CYC.5: 23 residues within 4Å: Chain F: I.61, Y.62, T.66, Y.73, T.74, T.75 Chain G: V.65, N.71, A.72, M.77, L.80, C.81, R.83, D.84, Y.87, Y.88, I.107, M.115, Y.116, L.119, T.121, P.122, A.125 21 PLIP interactions: 16 interactions with chain G, 5 interactions with chain F Hydrophobic interactions: G:L.80, G:L.80, G:Y.87, G:Y.88, G:I.107, G:L.119, G:A.125, F:Y.62, F:T.75 Hydrogen bonds: G:N.71, G:N.71, G:A.72, G:R.83, G:D.84, G:L.119, G:T.121, F:Y.62, F:Y.62, F:T.74 Salt bridges: G:R.83 pi-Cation interactions: G:R.83 CYC.6: 25 residues within 4Å: Chain H: N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, M.85, Y.87, L.112, T.115, Y.116, L.119, V.121, P.122, A.125, T.126 Chain O: R.3, Y.34, W.37, F.38, Q.41, Q.42, Q.45 24 PLIP interactions: 15 interactions with chain H, 9 interactions with chain O Hydrophobic interactions: H:R.77, H:A.80, H:D.84, H:Y.87, H:L.112, H:T.115, H:L.119, H:V.121, H:P.122, H:A.125, O:Y.34, O:F.38 Hydrogen bonds: H:R.83, H:D.84, O:Y.34, O:Y.34, O:Q.41, O:Q.42, O:Q.45 Salt bridges: H:R.76, H:R.77, H:R.83, O:R.3 pi-Stacking: O:F.38 CYC.7: 22 residues within 4Å: Chain I: V.65, N.71, A.72, M.77, L.80, C.81, R.83, D.84, Y.87, Y.88, I.107, M.115, Y.116, L.119, T.121, A.125 Chain L: K.53, I.61, Y.62, T.66, Y.73, T.74 22 PLIP interactions: 6 interactions with chain L, 16 interactions with chain I Hydrophobic interactions: L:I.61, L:Y.62, I:V.65, I:L.80, I:L.80, I:Y.87, I:Y.88, I:I.107, I:T.121, I:A.125 Hydrogen bonds: L:Y.62, L:Y.62, L:T.74, I:N.71, I:N.71, I:A.72, I:R.83, I:D.84, I:T.121 Salt bridges: L:K.53, I:R.83 pi-Stacking: I:Y.87 CYC.8: 26 residues within 4Å: Chain A: G.970, V.971, T.1118, L.1119, P.1120, Y.1124 Chain J: L.65, N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, M.85, Y.87, F.88, V.108, L.112, T.115, Y.116, L.119, V.121, A.125, T.126 24 PLIP interactions: 9 interactions with chain A, 15 interactions with chain J Hydrophobic interactions: A:V.971, A:T.1118, A:Y.1124, A:Y.1124, J:A.80, J:Y.87, J:F.88, J:V.108, J:L.112, J:T.115, J:Y.116, J:L.119, J:V.121, J:A.125 Hydrogen bonds: A:G.970, A:V.971, A:T.1118, A:T.1118, A:T.1118, J:R.83, J:R.83, J:D.84 Salt bridges: J:R.76, J:R.83 CYC.9: 22 residues within 4Å: Chain D: I.61, Y.62, T.66, Y.73, T.74, T.75 Chain K: V.65, N.71, M.77, L.80, C.81, R.83, D.84, Y.87, Y.88, I.107, M.115, Y.116, L.119, T.121, P.122, A.125 17 PLIP interactions: 4 interactions with chain D, 13 interactions with chain K Hydrophobic interactions: D:Y.62, D:T.75, K:V.65, K:L.80, K:L.80, K:Y.87, K:Y.88, K:L.119, K:A.125 Hydrogen bonds: D:Y.62, D:T.74, K:N.71, K:N.71, K:A.72, K:R.83, K:D.84 Salt bridges: K:R.83 CYC.10: 25 residues within 4Å: Chain A: S.1055, P.1056, Q.1074, S.1078, V.1081 Chain L: L.65, N.71, M.72, R.76, R.77, A.80, C.81, D.84, M.85, Y.87, F.88, Y.91, V.108, L.112, T.115, Y.116, L.119, V.121, A.125, T.126 14 PLIP interactions: 12 interactions with chain L, 2 interactions with chain A Hydrophobic interactions: L:A.80, L:Y.87, L:F.88, L:Y.91, L:L.112, L:L.112, L:T.115, L:L.119, L:V.121, L:A.125, A:P.1056 Hydrogen bonds: L:D.84, A:S.1055 Salt bridges: L:R.76 CYC.11: 23 residues within 4Å: Chain H: I.61, Y.62, T.66, Y.73, T.74, T.75 Chain M: V.65, N.71, A.72, M.77, L.80, C.81, R.83, D.84, Y.87, Y.88, I.107, M.115, Y.116, L.119, T.121, P.122, A.125 21 PLIP interactions: 9 interactions with chain H, 12 interactions with chain M Hydrophobic interactions: H:I.61, H:Y.62, H:T.66, H:Y.73, H:T.75, M:L.80, M:Y.87, M:Y.88, M:I.107, M:A.125 Hydrogen bonds: H:Y.62, H:S.63, H:T.66, H:T.74, M:A.72, M:R.83, M:D.84, M:L.119, M:T.121 Salt bridges: M:R.83 pi-Cation interactions: M:R.83 CYC.12: 20 residues within 4Å: Chain A: S.1023 Chain N: L.65, N.71, M.72, R.77, A.80, C.81, R.83, D.84, M.85, Y.87, F.88, R.107, V.108, L.112, Y.116, L.119, V.121, A.125, T.126 17 PLIP interactions: 4 interactions with chain A, 13 interactions with chain N Hydrogen bonds: A:S.1023, A:S.1023, A:S.1023, N:R.76, N:R.83, N:D.84 Salt bridges: A:K.1026, N:R.77, N:R.83 Hydrophobic interactions: N:A.80, N:Y.87, N:F.88, N:V.108, N:L.112, N:L.119, N:V.121, N:A.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Burtseva, A.D. et al., Structure and quenching of a bundle-shaped phycobilisome. Sci Adv (2025)

Release Date

2025-09-24

Peptides

Phycobiliprotein ApcE: A
Glr1262 protein: B
Allophycocyanin alpha subunit: CEGIKM
Allophycocyanin beta subunit: DFHJLN
Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core: O
Glr2806 protein: P

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

B
Z

C
A

E
C

G
E

I
G

K
I

M
K

D
B

F
D

H
F

J
H

L
J

N
L

O
M

P
X

Phycobiliprotein ApcE

Glr1262 protein

Allophycocyanin alpha subunit

Allophycocyanin beta subunit

Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core

Glr2806 protein

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