SMTL ID : 9v7l.1

Phycobilisome rod R1 from Gloeobacter violaceus PCC 7421

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.76 Å

Oligo State

hetero-1-1-12-12-1-mer

Ligands

36 x CYC: PHYCOCYANOBILIN(Covalent)

CYC.1: 18 residues within 4Å: Chain 0: L.24, Q.25, N.28 Chain C: N.35, K.36, L.38, D.39, V.142, N.143, P.145, V.148, T.149, R.150, G.151, C.153 Chain F: R.33, Q.145, T.148 Ligand excluded by PLIP CYC.2: 22 residues within 4Å: Chain B: H.37, E.38, P.39 Chain C: N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, R.108, C.109, L.113, T.116, Y.117, L.120, T.122, S.126, V.127 Ligand excluded by PLIP CYC.3: 20 residues within 4Å: Chain D: Y.60, L.66, M.72, G.73, N.78, K.81, C.82, R.84, D.85, H.88, Y.89, I.109, V.116, F.120, L.122, W.126, Y.127 Chain G: H.57, I.67, N.76 Ligand excluded by PLIP CYC.4: 16 residues within 4Å: Chain D: L.24, N.28 Chain E: N.35, K.36, L.38, D.39, V.142, P.145, V.148, T.149, R.150, G.151, C.153 Chain H: R.33, Q.145, E.149 Ligand excluded by PLIP CYC.5: 25 residues within 4Å: Chain E: L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, R.108, C.109, L.113, Y.117, L.120, T.122, S.126, A.130 Chain N: S.161, N.162, A.185, L.188, D.189, R.271 Ligand excluded by PLIP CYC.6: 18 residues within 4Å: Chain F: Y.60, L.66, G.73, N.78, K.81, C.82, R.84, D.85, H.88, Y.89, F.92, F.120, L.122, W.126 Chain M: H.57, I.67, Y.74, N.76 Ligand excluded by PLIP CYC.7: 16 residues within 4Å: Chain 0: R.33, Q.145 Chain F: L.24, N.28 Chain G: N.35, K.36, L.38, D.39, V.142, N.143, P.145, V.148, T.149, R.150, G.151, C.153 Ligand excluded by PLIP CYC.8: 19 residues within 4Å: Chain G: N.72, A.73, R.77, R.78, A.81, C.82, D.85, I.88, L.113, T.116, Y.117, L.120, T.122, S.126 Chain N: N.116, Y.118, A.246, S.248, L.252 Ligand excluded by PLIP CYC.9: 20 residues within 4Å: Chain H: Y.60, M.72, G.73, N.78, K.81, C.82, R.84, D.85, H.88, Y.89, F.92, V.116, F.120, L.122, W.126 Chain K: H.57, F.60, I.67, Y.74, N.76 Ligand excluded by PLIP CYC.10: 20 residues within 4Å: Chain B: T.5, G.6 Chain I: L.66, N.72, R.78, A.81, C.82, R.84, D.85, M.86, I.88, L.113, Y.117, L.120, T.122, P.123, S.126 Chain N: S.130, R.133, N.134 Ligand excluded by PLIP CYC.11: 19 residues within 4Å: Chain D: R.33, Q.145, E.149 Chain H: N.21, L.24, N.28 Chain I: K.32, N.35, K.36, L.38, D.39, V.142, N.143, P.145, V.148, T.149, R.150, G.151, C.153 Ligand excluded by PLIP CYC.12: 21 residues within 4Å: Chain C: H.57, I.67, Y.74, P.75, N.76 Chain J: Y.60, L.66, M.72, G.73, N.78, K.81, C.82, R.84, D.85, Y.89, I.109, V.116, F.120, L.122, W.126, Y.127 Ligand excluded by PLIP CYC.13: 21 residues within 4Å: Chain B: L.50, L.53, L.54, M.57 Chain K: N.72, A.73, R.77, R.78, C.82, R.84, D.85, M.86, I.88, R.108, C.109, L.113, Y.117, L.120, T.122, S.126, V.127 Ligand excluded by PLIP CYC.14: 15 residues within 4Å: Chain J: N.28 Chain K: N.35, K.36, L.38, D.39, V.142, N.143, P.145, V.148, T.149, G.151, C.153 Chain L: R.33, Q.145, E.149 Ligand excluded by PLIP CYC.15: 19 residues within 4Å: Chain E: H.57, Y.74, N.76, M.79 Chain L: Y.60, M.72, G.73, N.78, K.81, C.82, R.84, D.85, H.88, Y.89, F.92, F.120, L.122, W.126, Y.127 Ligand excluded by PLIP CYC.16: 25 residues within 4Å: Chain M: L.59, L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, R.108, C.109, L.113, T.116, Y.117, L.120, T.122, S.126, V.127 Chain N: F.224, K.225, Q.230, V.232 Ligand excluded by PLIP CYC.17: 18 residues within 4Å: Chain J: R.33, Q.145, E.149 Chain L: L.24, Q.25, N.28 Chain M: N.35, K.36, L.38, D.39, V.142, N.143, P.145, V.148, T.149, R.150, G.151, C.153 Ligand excluded by PLIP CYC.18: 19 residues within 4Å: Chain O: Y.60, M.72, G.73, N.78, K.81, C.82, R.84, D.85, H.88, Y.89, F.92, F.120, L.122, W.126, Y.127 Chain V: H.57, I.67, Y.74, N.76 Ligand excluded by PLIP CYC.19: 17 residues within 4Å: Chain O: L.24, Q.25, N.28 Chain P: N.35, K.36, L.38, D.39, V.142, N.143, P.145, V.148, T.149, R.150, G.151, C.153 Chain S: R.33, Q.145 Ligand excluded by PLIP CYC.20: 21 residues within 4Å: Chain A: S.143, L.144, R.146, N.147 Chain N: L.4 Chain P: L.66, N.72, A.73, R.78, A.81, C.82, R.84, D.85, M.86, R.108, L.113, Y.117, L.120, T.122, S.126, V.127 Ligand excluded by PLIP CYC.21: 18 residues within 4Å: Chain Q: Y.60, M.72, G.73, N.78, K.81, C.82, R.84, D.85, H.88, Y.89, V.116, F.120, L.122, W.126, Y.127 Chain T: H.57, Y.74, N.76 Ligand excluded by PLIP CYC.22: 15 residues within 4Å: Chain Q: N.28 Chain R: N.35, K.36, L.38, D.39, V.142, P.145, V.148, T.149, R.150, G.151, C.153 Chain U: R.33, Q.145, E.149 Ligand excluded by PLIP CYC.23: 21 residues within 4Å: Chain A: A.89, Y.239, Q.243, F.248 Chain R: L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, I.88, R.108, C.109, Y.117, L.120, T.122, S.126, V.127 Ligand excluded by PLIP CYC.24: 18 residues within 4Å: Chain S: Y.60, M.72, G.73, N.78, K.81, C.82, R.84, D.85, H.88, Y.89, F.92, F.120, L.122, W.126 Chain Z: H.57, Y.74, P.75, N.76 Ligand excluded by PLIP CYC.25: 16 residues within 4Å: Chain O: R.33, Q.145, T.148 Chain S: N.28 Chain T: N.35, K.36, L.38, D.39, V.142, N.143, P.145, V.148, T.149, R.150, G.151, C.153 Ligand excluded by PLIP CYC.26: 23 residues within 4Å: Chain A: S.174, N.175, N.176, A.198, L.201 Chain T: N.72, A.73, R.77, R.78, C.82, R.84, D.85, M.86, I.88, R.108, C.109, L.113, T.116, Y.117, L.120, T.122, S.126, V.127 Ligand excluded by PLIP CYC.27: 21 residues within 4Å: Chain U: Y.60, M.72, G.73, N.78, K.81, C.82, R.84, D.85, H.88, Y.89, F.92, I.109, V.116, F.120, L.122, W.126, Y.127 Chain X: H.57, I.67, Y.74, N.76 Ligand excluded by PLIP CYC.28: 20 residues within 4Å: Chain N: L.49, L.52, L.53, M.56, K.60 Chain V: N.72, A.73, R.78, A.81, C.82, R.84, D.85, M.86, C.109, L.113, T.116, Y.117, L.120, T.122, S.126 Ligand excluded by PLIP CYC.29: 17 residues within 4Å: Chain Q: R.33, Q.145, E.149 Chain U: L.24, N.28 Chain V: N.35, K.36, L.38, D.39, V.142, N.143, P.145, V.148, T.149, R.150, G.151, C.153 Ligand excluded by PLIP CYC.30: 21 residues within 4Å: Chain P: H.57, I.67, Y.74, N.76 Chain W: Y.60, L.66, M.72, G.73, N.78, K.81, C.82, R.84, D.85, H.88, Y.89, I.109, V.116, F.120, L.122, W.126, Y.127 Ligand excluded by PLIP CYC.31: 23 residues within 4Å: Chain N: P.23, H.28, D.34, T.35, Y.36, P.38 Chain X: N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, L.113, Y.117, L.120, T.122, S.126, V.127, A.130 Ligand excluded by PLIP CYC.32: 17 residues within 4Å: Chain W: N.28 Chain X: N.35, K.36, L.38, D.39, V.142, N.143, P.145, V.148, T.149, R.150, G.151, C.153 Chain Y: R.33, Q.145, T.148, E.149 Ligand excluded by PLIP CYC.33: 16 residues within 4Å: Chain R: H.57, N.76 Chain Y: Y.60, M.72, G.73, N.78, K.81, C.82, R.84, D.85, H.88, Y.89, F.92, F.120, L.122, W.126 Ligand excluded by PLIP CYC.34: 17 residues within 4Å: Chain W: R.33, Q.145, E.149 Chain Y: L.24, N.28 Chain Z: N.35, K.36, L.38, D.39, V.142, N.143, P.145, V.148, T.149, R.150, G.151, C.153 Ligand excluded by PLIP CYC.35: 22 residues within 4Å: Chain A: T.130, Y.131, A.259, S.261, T.263, D.264, R.265 Chain Z: N.72, A.73, R.77, R.78, A.81, C.82, D.85, M.86, I.88, R.108, T.116, Y.117, L.120, T.122, S.126 Ligand excluded by PLIP CYC.36: 19 residues within 4Å: Chain 0: Y.60, M.72, G.73, N.78, K.81, C.82, R.84, D.85, Y.89, F.92, F.120, L.122, W.126, Y.127 Chain I: H.57, I.67, Y.74, P.75, N.76 Ligand excluded by PLIP

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

Glr1262 protein: A
Phycocyanin-associated rod linker protein: B
Phycocyanin beta chain: CEGIKMPRTVXZ
Phycocyanin alpha chain: DFHJLOQSUWY0
Phycocyanin-associated rod linker protein: N

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
Z

C
B

E
D

G
F

I
H

K
J

M
L

P
O

R
Q

T
S

V
U

X
W

Z
Y

D
C

F
E

H
G

J
I

L
K

O
N

Q
P

S
R

U
T

W
V

Y
X

0
a

N
M

Glr1262 protein

Phycocyanin-associated rod linker protein

Phycocyanin beta chain

Phycocyanin alpha chain

Phycocyanin-associated rod linker protein

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