SMTL ID : 7scb.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-10-11-1-1-2-1-1-1-1-mer

Ligands

24 x CYC: PHYCOCYANOBILIN(Covalent)

CYC.1: 25 residues within 4Å: Chain A: I.65, N.71, A.72, M.77, T.80, C.81, R.83, D.84, M.85, Y.87, Y.88, L.91, M.115, Y.116, L.119, T.121, A.125, S.129 Chain F: K.53, L.61, Y.62, T.66, Y.73, T.75, Y.78 Ligand excluded by PLIP CYC.2: 27 residues within 4Å: Chain B: L.60, N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, Y.88, Y.91, R.107, L.112, T.115, L.119, V.121, P.122, S.125, T.126 Chain Z: Y.304, S.307, Q.308, R.310, N.311, D.313 Ligand excluded by PLIP CYC.3: 23 residues within 4Å: Chain B: L.61, Y.62, T.66, Y.73, T.75, Y.78 Chain C: L.58, I.65, N.71, M.77, T.80, C.81, R.83, D.84, M.85, Y.87, Y.88, M.115, Y.116, L.119, T.121, A.125, V.126 Ligand excluded by PLIP CYC.4: 25 residues within 4Å: Chain D: L.60, N.71, M.72, R.77, C.81, R.83, D.84, L.85, Y.87, Y.88, Y.91, V.108, L.112, Y.116, L.119, V.121, S.125, T.126 Chain X: P.11, S.12, R.15, L.22, Q.23, N.24, T.25 Ligand excluded by PLIP CYC.5: 24 residues within 4Å: Chain D: L.61, Y.62, T.66, Y.73, T.74, T.75 Chain E: Y.65, N.71, Q.77, Q.80, C.81, R.83, D.84, Y.85, W.87, Y.88, L.91, T.107, G.108, M.115, Y.116, L.119, V.121, M.126 Ligand excluded by PLIP CYC.6: 24 residues within 4Å: Chain F: L.60, N.71, M.72, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, Y.91, L.112, Y.116, L.119, V.121, S.125, T.126 Chain X: R.2, Y.33, W.36, F.37, Q.40, Q.41, M.44 Ligand excluded by PLIP CYC.7: 23 residues within 4Å: Chain G: I.65, N.71, A.72, M.77, T.80, C.81, R.83, D.84, Y.87, Y.88, L.91, M.115, Y.116, L.119, T.121, A.125, V.126 Chain K: L.61, Y.62, T.66, Y.73, T.75, Y.78 Ligand excluded by PLIP CYC.8: 25 residues within 4Å: Chain H: 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, Y.116, L.119, V.121, S.125, T.126 Chain Z: I.338, N.339, S.340, R.358, Q.362, F.365, I.431 Ligand excluded by PLIP CYC.9: 23 residues within 4Å: Chain H: L.61, Y.62, T.66, Y.73, T.75 Chain I: I.65, N.71, A.72, M.77, T.80, C.81, R.83, D.84, M.85, Y.87, Y.88, L.91, M.115, Y.116, L.119, T.121, A.125, S.129 Ligand excluded by PLIP CYC.10: 31 residues within 4Å: Chain J: L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, Y.88, Y.89, Y.92, R.108, V.109, T.116, Y.117, L.120, V.122, P.123, P.126, T.127 Chain Z: P.14, Q.249, L.251, L.253, Y.257, L.401, Q.406, E.407, C.408 Ligand excluded by PLIP CYC.11: 25 residues within 4Å: Chain K: 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.91, R.107, L.112, T.115, Y.116, L.119, V.121, S.125, T.126 Chain Z: R.292, Y.298, Y.420, F.424 Ligand excluded by PLIP CYC.12: 25 residues within 4Å: Chain 2: R.100 Chain L: I.65, N.71, A.72, M.77, T.80, C.81, R.83, D.84, Y.87, Y.88, L.91, G.108, M.115, Y.116, L.119, T.121, A.125, V.126, S.129 Chain Q: L.61, Y.62, T.66, Y.73, Y.78 Ligand excluded by PLIP CYC.13: 27 residues within 4Å: Chain M: L.60, V.65, N.71, M.72, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, Y.91, R.107, L.112, Y.116, L.119, V.121, P.122, S.125, T.126 Chain Z: I.483, L.484, I.485, H.486, A.490, N.493, V.495 Ligand excluded by PLIP CYC.14: 24 residues within 4Å: Chain M: L.61, Y.62, T.66, Y.73, T.75, Y.78 Chain N: I.65, N.71, A.72, M.77, T.80, C.81, R.83, D.84, M.85, Y.87, Y.88, L.91, M.115, Y.116, L.119, T.121, A.125, S.129 Ligand excluded by PLIP CYC.15: 27 residues within 4Å: Chain O: 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, V.108, L.112, T.115, Y.116, L.119, V.121, S.125, T.126 Chain Z: I.456, Q.457, F.458, G.459, R.553 Ligand excluded by PLIP CYC.16: 24 residues within 4Å: Chain 1: I.11 Chain O: L.61, Y.62, T.66, Y.73, T.75, Y.78 Chain P: I.65, N.71, A.72, M.77, T.80, C.81, R.83, D.84, M.85, Y.87, Y.88, M.115, Y.116, L.119, T.121, A.125, S.129 Ligand excluded by PLIP CYC.17: 26 residues within 4Å: Chain Q: L.60, V.65, N.71, M.72, R.77, A.80, C.81, D.84, L.85, Y.87, R.107, V.108, L.112, T.115, Y.116, L.119, V.121, S.125, T.126 Chain Z: Y.447, Y.597, V.598, C.599, R.617, N.621, F.624 Ligand excluded by PLIP CYC.18: 22 residues within 4Å: Chain R: I.65, N.71, A.72, M.77, T.80, C.81, R.83, D.84, M.85, Y.87, Y.88, M.115, Y.116, L.119, T.121, A.125, V.126 Chain W: L.61, Y.62, T.66, Y.73, Y.78 Ligand excluded by PLIP CYC.19: 28 residues within 4Å: Chain S: 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.91, V.108, L.112, Y.116, L.119, V.121, P.122, S.125, T.126 Chain Y: R.2, Y.33, W.36, F.37, Q.40, Q.41, M.44 Ligand excluded by PLIP CYC.20: 23 residues within 4Å: Chain S: L.61, Y.62, T.66, Y.73, T.74, T.75 Chain T: 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, A.125 Ligand excluded by PLIP CYC.21: 23 residues within 4Å: Chain U: L.60, N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, Y.91, R.107, V.108, L.112, L.119, V.121, S.125, T.126 Chain Z: K.533, I.566, E.569, N.570 Ligand excluded by PLIP CYC.22: 25 residues within 4Å: Chain U: L.61, Y.62, T.66, Y.73, T.75, Y.78 Chain V: I.65, N.71, A.72, M.77, T.80, C.81, R.83, D.84, Y.87, Y.88, L.91, G.108, M.115, Y.116, L.119, T.121, A.125, V.126, S.129 Ligand excluded by PLIP CYC.23: 26 residues within 4Å: Chain W: L.60, N.71, M.72, R.76, R.77, C.81, R.83, D.84, L.85, Y.87, Y.91, L.112, T.115, Y.116, L.119, V.121, S.125, T.126 Chain Y: P.11, S.12, Q.13, R.17, R.20, E.21, L.22, T.25 Ligand excluded by PLIP CYC.24: 19 residues within 4Å: Chain J: I.67, T.75, T.76, F.79 Chain Z: Y.144, N.148, K.151, S.152, R.154, D.155, M.156, W.158, F.159, N.178, L.182, I.186, A.189, C.190, T.195 Ligand excluded by PLIP

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

45D.25: 34 residues within 4Å: Chain 1: E.34, L.37, A.38, I.40, W.41, 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, I.125, P.126, Y.129, I.151, L.154, E.174, V.176 Chain P: P.68, G.69, Y.73 30 PLIP interactions: 28 interactions with chain 1, 2 interactions with chain P Hydrophobic interactions: 1:L.37, 1:L.37, 1:L.37, 1:A.38, 1:I.40, 1:I.40, 1:W.41, 1:Y.44, 1:A.54, 1:A.55, 1:A.58, 1:A.59, 1:T.80, 1:L.107, 1:L.107, 1:L.107, 1:W.110, 1:W.110, 1:W.110, 1:Y.111, 1:L.113, 1:I.125, 1:P.126, 1:Y.129, 1:Y.129, 1:I.151, 1:L.154, 1:L.154, P:P.68 Hydrogen bonds: P:G.69

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: ACGILNPRTV
Allophycocyanin beta chain: BDFHKMOQSUW
Allophycocyanin subunit alpha-B: E
Allophycocyanin subunit beta-18: J
Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core: XY
Phycobiliprotein ApcE: Z
Phycobilisome rod-core linker polypeptide CpcG: 0
Orange carotenoid-binding protein: 1
Sll1873 protein: 2

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AA

C
AC

G
AH

I
AJ

L
AN

N
AP

P
AR

R
AU

T
AW

V
AY

B
AB

D
AD

F
AF

H
AI

K
AL

M
AO

O
AQ

Q
AS

S
AV

U
AX

W
AZ

E
AE

J
AK

X
BB

Y
BC

Z
BE

0
BG

1
BH

2
BI

Allophycocyanin alpha chain

Allophycocyanin beta chain

Allophycocyanin subunit alpha-B

Allophycocyanin subunit beta-18

Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core

Phycobiliprotein ApcE

Phycobilisome rod-core linker polypeptide CpcG

Orange carotenoid-binding protein

Sll1873 protein

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