SMTL ID : 6dhf.1

RT XFEL structure of the one-flash state of Photosystem II (1F, S2-rich) at 2.08 Angstrom resolution

Coordinates
PDB Format
Method
X-RAY DIFFRACTION 2.08 Å
Oligo State
hetero-2-2-2-2-2-2-2-2-2-2-2-2-2-2-2-2-2-2-2-2-mer
Ligands
2 x FE2: FE (II) ION(Non-covalent)
4 x CL: CHLORIDE ION(Non-functional Binders)
2 x BCT: BICARBONATE ION(Non-functional Binders)
70 x CLA: CHLOROPHYLL A(Non-covalent)
4 x PHO: PHEOPHYTIN A(Non-covalent)
22 x BCR: BETA-CAROTENE(Non-covalent)
4 x PL9: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE(Non-covalent)
8 x SQD: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL(Non-covalent)
10 x DGD: DIGALACTOSYL DIACYL GLYCEROL (DGDG)(Non-covalent)
2 x OEX: CA-MN4-O5 CLUSTER(Covalent)
31 x UNL: UNKNOWN LIGAND(Non-functional Binders)
13 x LMG: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE(Non-covalent)
10 x LHG: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE(Non-covalent)
2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
2 x HEC: HEME C(Covalent)
Links
RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP
Citation
Kern, J. et al., Structures of the intermediates of Kok's photosynthetic water oxidation clock. Nature (2018)
Release Date
2018-11-21
Peptides
Photosystem II protein D1 1: AU
Photosystem II CP47 reaction center protein: BV
Photosystem II CP43 reaction center protein: CW
Photosystem II D2 protein: DX
Cytochrome b559 subunit alpha: EY
Cytochrome b559 subunit beta: FZ
Photosystem II reaction center protein H: G0
Photosystem II reaction center protein I: H1
Photosystem II reaction center protein J: I2
Photosystem II reaction center protein K: J3
Photosystem II reaction center protein L: K4
Photosystem II reaction center protein M: L5
Photosystem II manganese-stabilizing polypeptide: M6
Photosystem II reaction center protein T: N7
Photosystem II 12 kDa extrinsic protein: O8
Cytochrome c-550: P9
Photosystem II reaction center protein Ycf12: Qa
Photosystem II reaction center X protein: Rb
Photosystem II reaction center protein Z: Sc
Photosystem II protein Y: Td
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
U
a
B
B
V
b
C
C
W
c
D
D
X
d
E
E
Y
e
F
F
Z
f
G
H
0
h
H
I
1
i
I
J
2
j
J
K
3
k
K
L
4
l
L
M
5
m
M
O
6
o
N
T
7
t
O
U
8
u
P
V
9
v
Q
Y
a
y
R
X
b
x
S
Z
c
z
T
R
d
r
Membrane
We predict this structure to be a membrane protein.

Photosystem II protein D1 1

Toggle Identical (AU)

Photosystem II CP47 reaction center protein

Toggle Identical (BV)

Photosystem II CP43 reaction center protein

Photosystem II D2 protein

Toggle Identical (DX)

Cytochrome b559 subunit alpha

Cytochrome b559 subunit beta

Toggle Identical (FZ)

Photosystem II reaction center protein H

Photosystem II reaction center protein I

Toggle Identical (H1)

Photosystem II reaction center protein J

Toggle Identical (I2)

Photosystem II reaction center protein K

Toggle Identical (J3)

Photosystem II reaction center protein L

Photosystem II reaction center protein M

Photosystem II manganese-stabilizing polypeptide

Toggle Identical (M6)

Photosystem II reaction center protein T

Toggle Identical (N7)

Photosystem II 12 kDa extrinsic protein

Toggle Identical (O8)

Cytochrome c-550

Toggle Identical (P9)

Photosystem II reaction center protein Ycf12

Photosystem II reaction center X protein

Toggle Identical (Rb)

Photosystem II reaction center protein Z

Toggle Identical (Sc)

Photosystem II protein Y

Related Entries With Identical Sequence

1izl.1 | 1mz4.1 | 1s5l.1 | 1s5l.2 | 2axt.1 | 3a0b.1 | 3a0h.1 | 3kzi.1 | 3wu2.1 | 4fby.1 | 4il6.1 | 4ixq.1 | 4ixr.1 | 4pbu.1 | 4pj0.1 | 4rvy.1 | 4tnh.1 | 4tni.1 | 4tnj.1 | 4tnk.1 | 4ub6.1 | 4ub6.2 | 4ub8.1 | 4ub8.2 | 4v62.1 | 4v62.2 | 4v82.1 | 5b5e.1 | 5b66.1 | 5e79.1  more...