National Center for
Biotechnology Information

5B5E: Crystal structure analysis of Photosystem II complex

PDB ID:	5B5E Download
MMDB ID:	146902
PDB Deposition Date:	2016/5/2
Updated in MMDB:	2022/11
Experimental Method:	x-ray diffraction
Resolution:	1.87 Å
Source Organism:	Thermostichus vulcanus
Similar Structures:

Biological Unit for 5B5E: 38-meric; determined by author

Molecular Components in 5B5E
Label	Count	Molecule
Proteins (38 molecules)
A a	2	Photosystem II Protein D1
B b	2	Photosystem II Cp47 Reaction Center Protein
C c	2	Photosystem II Cp43 Reaction Center Protein
D d	2	Photosystem II D2 Protein
E e	2	Cytochrome B559 Subunit Alpha
F f	2	Cytochrome B559 Subunit Beta
H h	2	Photosystem II Reaction Center Protein H
I i	2	Photosystem II Reaction Center Protein I
J j	2	Photosystem II Reaction Center Protein J
K k	2	Photosystem II Reaction Center Protein K
L l	2	Photosystem II Reaction Center Protein L
M m	2	Photosystem II Reaction Center Protein M
O o	2	Photosystem II Manganese-stabilizing Polypeptide
T t	2	Photosystem II Reaction Center Protein T
U u	2	Photosystem II 12 KDA Extrinsic Protein
V v	2	Cytochrome C-550
Y y	2	Photosystem II Reaction Center Protein Ycf12
X x	2	Photosystem II Reaction Center Protein X
Z z	2	Photosystem II Reaction Center Protein Z
Chemicals and Non-standard biopolymers (366 molecules)
1	2	CA-MN4-O5 CLUSTER (Link to PubChem not yet available)
2	2	FE (II) ION (Link to PubChem not yet available)
3	4	CHLORIDE ION (Link to PubChem not yet available)
4	70	CHLOROPHYLL A (Link to PubChem not yet available)
5	4	PHEOPHYTIN A (Link to PubChem not yet available)
6	20	BETA-CAROTENE (Link to PubChem not yet available)
7	8	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL (Link to PubChem not yet available)
8	4	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 (Link to PubChem not yet available)
9	14	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE (Link to PubChem not yet available)
10	53	UNKNOWN LIGAND (Link to PubChem not yet available)
11	16	DODECYL-BETA-D-MALTOSIDE (Link to PubChem not yet available)
12	112	DIMETHYL SULFOXIDE (Link to PubChem not yet available)
13	2	BICARBONATE ION (Link to PubChem not yet available)
14	5	CALCIUM ION (Link to PubChem not yet available)
15	12	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE (Link to PubChem not yet available)
16	20	heptyl 1-thio-beta-D-glucopyranoside (Link to PubChem not yet available)
17	10	DIGALACTOSYL DIACYL GLYCEROL (DGDG) (Link to PubChem not yet available)
18	2	PROTOPORPHYRIN IX CONTAINING FE (Link to PubChem not yet available)
19	2	(3R)-beta,beta-caroten-3-ol (Link to PubChem not yet available)
20	2	MAGNESIUM ION (Link to PubChem not yet available)
21	2	HEME C (Link to PubChem not yet available)

* Click molecule labels to explore molecular sequence information.

Citing MMDB

Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. " MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan; 42(Database issue):D297-303