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SMTL ID : 5ws5.1 (1 other biounit)

Native XFEL structure of photosystem II (preflash dark dataset)

Coordinates
PDB Format
Method
X-RAY DIFFRACTION 2.35 Å
Oligo State
hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer
Ligands
1 x FE2: FE (II) ION(Non-covalent)
2 x CL: CHLORIDE ION(Non-functional Binders)
35 x CLA: CHLOROPHYLL A(Non-covalent)
2 x PHO: PHEOPHYTIN A(Non-covalent)
11 x BCR: BETA-CAROTENE(Non-covalent)
4 x SQD: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL(Non-covalent)
5 x GOL: GLYCEROL(Non-functional Binders)
1 x OEX: CA-MN4-O5 CLUSTER(Covalent)
2 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)
9 x UNL: UNKNOWN LIGAND
1 x BCT: BICARBONATE ION(Non-functional Binders)
6 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)
6 x LMG: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE(Non-covalent)
6 x HTG: heptyl 1-thio-beta-D-glucopyranoside(Non-covalent)
4 x DGD: DIGALACTOSYL DIACYL GLYCEROL (DGDG)(Non-covalent)
3 x CA: CALCIUM ION(Non-covalent)
5 x LHG: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE(Non-covalent)
1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
1 x MG: MAGNESIUM ION(Non-covalent)
1 x HEC: HEME C(Covalent)
Links
RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP
Citation
Suga, M. et al., Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL. Nature (2017)
Release Date
2017-03-15
Peptides
Photosystem II D1 protein: A
Photosystem II CP47 reaction center protein: B
Photosystem II CP43 protein: C
Photosystem II D2 protein: D
Cytochrome b559 subunit alpha: E
Cytochrome b559 subunit beta: F
Photosystem II reaction center protein H: G
Photosystem II reaction center protein I: H
Photosystem II reaction center protein J: I
Photosystem II protein K: J
Photosystem II reaction center protein L: K
Photosystem II protein M: L
Photosystem II manganese-stabilizing polypeptide: M
Photosystem II reaction center protein T: N
Photosystem II 12 kDa extrinsic protein: O
Cytochrome c-550: P
Photosystem II reaction center protein X: Q
Photosystem II reaction center protein Ycf12: R
Photosystem II reaction center protein Z: S
Photosystem II protein Y: T
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B
C
C
D
D
E
E
F
F
G
H
H
I
I
J
J
K
K
L
L
M
M
O
N
T
O
U
P
V
Q
X
R
Y
S
Z
T
R
Membrane
We predict this structure to be a membrane protein.

Photosystem II D1 protein

Photosystem II CP47 reaction center protein

Photosystem II CP43 protein

Photosystem II D2 protein

Cytochrome b559 subunit alpha

Cytochrome b559 subunit beta

Photosystem II reaction center protein H

Photosystem II reaction center protein I

Photosystem II reaction center protein J

Photosystem II protein K

Photosystem II reaction center protein L

Photosystem II protein M

Photosystem II manganese-stabilizing polypeptide

Photosystem II reaction center protein T

Photosystem II 12 kDa extrinsic protein

Cytochrome c-550

Photosystem II reaction center protein X

Photosystem II reaction center protein Ycf12

Photosystem II reaction center protein Z

Photosystem II protein Y

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1izl.1 | 1mz4.1 | 1s5l.1 | 1s5l.2 | 1w5c.1 | 1w5c.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  more...