SMTL ID : 7scc.1

T-cylinder of Synechocystis PCC 6803 Phycobilisome, complex with OCP - local refinement

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-12-12-2-2-4-4-mer

Ligands

24 x CYC: PHYCOCYANOBILIN(Covalent)

CYC.1: 25 residues within 4Å: Chain A: L.58, I.65, N.71, A.72, M.77, T.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, V.126 Chain F: L.61, Y.62, T.66, Y.73, T.74, Y.78 Ligand excluded by PLIP CYC.2: 26 residues within 4Å: Chain B: V.65, N.71, R.76, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, Y.88, Y.91, R.107, V.108, L.112, T.115, Y.116, L.119, V.121, P.122, S.125, T.126 Chain N: A.762, S.765, S.768, N.769 Ligand excluded by PLIP CYC.3: 22 residues within 4Å: Chain B: L.61, Y.62, S.63, T.66, T.75 Chain C: L.58, I.65, N.71, M.77, T.80, C.81, R.83, D.84, Y.87, I.107, G.108, M.115, L.119, T.121, P.122, A.125, V.126 Ligand excluded by PLIP CYC.4: 29 residues within 4Å: Chain D: L.60, V.65, N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, Y.87, Y.88, Y.91, R.107, L.112, Y.116, L.119, V.121, P.122, S.125, T.126 Chain M: P.11, S.12, R.17, Q.19, R.20, E.21, L.22, T.25 Ligand excluded by PLIP CYC.5: 26 residues within 4Å: Chain D: L.61, Y.62, T.66, Y.73, T.74, T.75 Chain E: L.58, F.59, I.65, N.71, A.72, M.77, T.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, V.126 Ligand excluded by PLIP CYC.6: 23 residues within 4Å: Chain F: V.65, N.71, R.76, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, Y.88, L.112, L.119, P.122, S.125, T.126 Chain M: R.2, Y.33, W.36, F.37, Q.40, Q.41, M.44 Ligand excluded by PLIP CYC.7: 27 residues within 4Å: Chain G: I.65, N.71, M.77, T.80, C.81, R.83, D.84, M.85, Y.87, Y.88, I.107, G.108, Y.116, L.119, T.121, P.122, A.125, V.126, S.129 Chain L: L.61, Y.62, T.66, Y.73, T.74, T.75, Y.78 Chain R: R.201 Ligand excluded by PLIP CYC.8: 26 residues within 4Å: Chain H: L.60, V.65, N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, Y.88, R.107, L.112, Y.116, L.119, V.121, S.125, T.126 Chain N: P.796, N.797, T.798, Q.816, Q.820, N.823 Ligand excluded by PLIP CYC.9: 25 residues within 4Å: Chain H: L.61, Y.62, T.66, Y.73, T.74, T.75 Chain I: L.58, I.65, N.71, A.72, M.77, T.80, C.81, R.83, D.84, Y.87, Y.88, I.107, M.115, L.119, T.121, P.122, A.125, V.126 Chain Q: R.201 Ligand excluded by PLIP CYC.10: 26 residues within 4Å: Chain J: N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, Y.87, Y.88, Y.91, R.107, L.112, T.115, Y.116, L.119, V.121, P.122, S.125, T.126 Chain N: G.713, V.714, R.718, T.860, L.861, F.866 Ligand excluded by PLIP CYC.11: 25 residues within 4Å: Chain J: L.61, Y.62, T.66, Y.73, T.74, T.75 Chain K: L.58, N.71, A.72, M.77, T.80, C.81, R.83, D.84, Y.87, Y.88, I.107, G.108, M.115, Y.116, L.119, T.121, P.122, A.125, V.126 Ligand excluded by PLIP CYC.12: 26 residues within 4Å: Chain L: L.60, V.65, N.71, M.72, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, R.107, V.108, L.112, T.115, Y.116, L.119, V.121, P.122, S.125, T.126 Chain N: R.749, Y.754, L.876, T.877, K.878 Ligand excluded by PLIP CYC.14: 25 residues within 4Å: Chain S: L.58, I.65, N.71, A.72, M.77, T.80, C.81, R.83, D.84, Y.87, Y.88, M.115, Y.116, L.119, T.121, P.122, A.125, V.126 Chain X: L.61, Y.62, T.66, Y.73, T.74, T.75, Y.78 Ligand excluded by PLIP CYC.15: 25 residues within 4Å: Chain 5: A.762, S.765, K.766, N.769 Chain T: V.65, N.71, R.76, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, Y.88, Y.91, V.108, L.112, T.115, Y.116, L.119, V.121, P.122, S.125, T.126 Ligand excluded by PLIP CYC.16: 24 residues within 4Å: Chain T: L.61, Y.62, T.66, T.74, T.75 Chain U: L.58, I.65, N.71, M.77, T.80, C.81, R.83, D.84, Y.87, Y.88, I.107, G.108, M.115, Y.116, L.119, T.121, P.122, A.125, V.126 Ligand excluded by PLIP CYC.17: 27 residues within 4Å: Chain 4: S.12, R.17, R.20, E.21, L.22, T.25 Chain V: L.60, V.65, N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, Y.87, Y.88, Y.91, R.107, L.112, Y.116, L.119, V.121, P.122, S.125, T.126 Ligand excluded by PLIP CYC.18: 26 residues within 4Å: Chain V: Y.62, T.66, Y.73, T.74, T.75 Chain W: L.58, F.59, I.65, N.71, A.72, M.77, T.80, C.81, R.83, D.84, Y.87, Y.88, L.91, I.107, G.108, M.115, L.119, T.121, P.122, A.125, V.126 Ligand excluded by PLIP CYC.19: 30 residues within 4Å: Chain 4: R.2, Y.33, W.36, F.37, Q.40, Q.41, M.44, G.61 Chain X: V.65, N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, Y.88, R.107, V.108, L.112, T.115, Y.116, L.119, V.121, P.122, S.125, T.126 Ligand excluded by PLIP CYC.20: 24 residues within 4Å: Chain 3: L.61, Y.62, T.66, Y.73, T.74 Chain 9: R.201 Chain Y: L.58, F.59, I.65, N.71, A.72, M.77, T.80, C.81, D.84, Y.87, Y.88, I.107, G.108, L.119, T.121, P.122, A.125, V.126 Ligand excluded by PLIP CYC.21: 26 residues within 4Å: Chain 5: N.797, T.798, Q.816, Q.820, N.823 Chain Z: L.60, V.65, N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, Y.88, Y.91, L.112, Y.116, L.119, V.121, P.122, S.125, T.126 Ligand excluded by PLIP CYC.22: 26 residues within 4Å: Chain 0: L.58, I.65, N.71, A.72, M.77, T.80, C.81, R.83, D.84, Y.87, Y.88, I.107, G.108, M.115, Y.116, L.119, T.121, P.122, A.125, V.126 Chain 8: R.201 Chain Z: L.61, Y.62, T.66, T.74, T.75 Ligand excluded by PLIP CYC.23: 26 residues within 4Å: Chain 1: L.60, N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, Y.87, Y.88, Y.91, R.107, L.112, V.121, P.122, S.125, T.126 Chain 5: G.713, V.714, R.718, T.860, L.861, P.862, A.863, F.866 Ligand excluded by PLIP CYC.24: 25 residues within 4Å: Chain 1: L.61, Y.62, T.66, Y.73, T.74, T.75, Y.78 Chain 2: L.58, N.71, A.72, M.77, T.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, V.126 Ligand excluded by PLIP CYC.25: 24 residues within 4Å: Chain 3: L.60, V.65, N.71, M.72, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, R.107, L.112, T.115, Y.116, L.119, V.121, P.122, S.125, T.126 Chain 5: R.749, Y.754, T.877, K.878 Ligand excluded by PLIP

2 x 45D: beta,beta-carotene-4,4'-dione(Non-covalent)

45D.13: 37 residues within 4Å: Chain A: P.68, G.69, Y.73 Chain O: E.34, L.37, A.38, I.40, W.41, A.43, Y.44, M.47, T.52, I.53, A.54, A.55, P.56, A.58, A.59, T.80, M.83, N.104, L.107, G.108, W.110, Y.111, L.113, G.114, M.117, P.124, I.125, P.126, Y.129, I.151, L.154, E.174, P.175, V.177 21 PLIP interactions: 21 interactions with chain O Hydrophobic interactions: O:L.37, O:L.37, O:I.40, O:W.41, O:Y.44, O:A.54, O:A.58, O:T.80, O:L.107, O:L.107, O:W.110, O:W.110, O:Y.111, O:L.113, O:I.125, O:P.126, O:Y.129, O:Y.129, O:L.154, O:V.177 Hydrogen bonds: O:V.177 45D.26: 39 residues within 4Å: Chain 7: E.34, L.37, A.38, I.40, W.41, A.43, Y.44, M.47, T.52, I.53, A.54, A.55, P.56, A.58, A.59, T.80, M.83, N.104, L.107, G.108, W.110, Y.111, L.113, G.114, M.117, P.124, I.125, P.126, Y.129, I.151, L.154, R.155, E.174, P.175, V.177 Chain S: P.68, G.69, G.70, Y.73 22 PLIP interactions: 20 interactions with chain 7, 2 interactions with chain S Hydrophobic interactions: 7:E.34, 7:L.37, 7:L.37, 7:L.37, 7:W.41, 7:Y.44, 7:A.54, 7:A.58, 7:T.80, 7:L.107, 7:L.107, 7:W.110, 7:W.110, 7:Y.111, 7:L.113, 7:I.125, 7:P.126, 7:Y.129, 7:Y.129, 7:L.154 Hydrogen bonds: S:G.69, S:G.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dominguez-Martin, M.A. et al., Structures of a phycobilisome in light-harvesting and photoprotected states. Nature (2022)

Release Date

2022-08-31

Peptides

Allophycocyanin alpha chain: ACEGIKSUWY02
Allophycocyanin beta chain: BDFHJLTVXZ13
Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core: M4
Phycobiliprotein ApcE: N5
Orange carotenoid-binding protein: OP67
Phycobilisome rod-core linker polypeptide CpcG: QR89

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AA

C
AC

E
AE

G
AH

I
AJ

K
AL

S
AW

U
AY

W
BA

Y
BD

0
BF

2
BH

B
AB

D
AD

F
AF

H
AI

J
AK

L
AM

T
AX

V
AZ

X
BB

Z
BE

1
BG

3
BI

M
AO

4
BK

N
AQ

5
BM

O
AS

P
AT

6
BO

7
BP

Q
AU

R
AV

8
BQ

9
BR

Allophycocyanin alpha chain

Allophycocyanin beta chain

Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core

Phycobiliprotein ApcE

Orange carotenoid-binding protein

Phycobilisome rod-core linker polypeptide CpcG

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