4UB6: Native structure of photosystem II (dataset-1) by a femtosecond X-ray laser

PDB ID: 4UB6Download
MMDB ID: 125274
PDB Deposition Date: 2014/8/12
Updated in MMDB: 2014/12
Experimental Method:
x-ray diffraction
Resolution: 1.95  Å
Source Organism:
Similar Structures:
Biological Unit for 4UB6: eicosameric; determined by author
Molecular Components in 4UB6
Label Count Molecule
Proteins (20 molecules)
1
Photosystem Q(b) Protein
Molecule annotation
1
Photosystem II Cp47 Chlorophyll Apoprotein
Molecule annotation
1
Photosystem II 44 KDA Reaction Center Protein
Molecule annotation
1
Photosystem II D2 Protein
Molecule annotation
1
Cytochrome B559 Subunit Alpha
Molecule annotation
1
Cytochrome B559 Subunit Beta
Molecule annotation
1
Photosystem II Reaction Center Protein H
Molecule annotation
1
Photosystem II Reaction Center Protein I
Molecule annotation
1
Photosystem II Reaction Center Protein J
Molecule annotation
1
Photosystem II Reaction Center Protein K
Molecule annotation
1
Photosystem II Reaction Center Protein L
Molecule annotation
1
Photosystem II Reaction Center Protein M
Molecule annotation
1
Photosystem II Manganese-stabilizing Polypeptide
Molecule annotation
1
Photosystem II Reaction Center Protein T
Molecule annotation
1
Photosystem II 12 KDA Extrinsic Protein
Molecule annotation
1
Cytochrome C-550
Molecule annotation
1
Photosystem II Reaction Center Protein Ycf12
Molecule annotation
1
Photosystem II Reaction Center Protein X
Molecule annotation
1
Photosystem II Reaction Center Protein Z
Molecule annotation
1
Photosystem II Protein Y
Molecule annotation
Chemicals and Non-standard biopolymers (139 molecules)
1
1
FE (II) ION (Link to PubChem not yet available)FE (II) ION
2
2
CHLORIDE ION (Link to PubChem not yet available)CHLORIDE ION
3
1
BICARBONATE ION (Link to PubChem not yet available)BICARBONATE ION
4
36
CHLOROPHYLL A (Link to PubChem not yet available)CHLOROPHYLL A
5
2
PHEOPHYTIN A (Link to PubChem not yet available)PHEOPHYTIN A
6
14
BETA-CAROTENE (Link to PubChem not yet available)BETA-CAROTENE
7
6
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL (Link to PubChem not yet available)1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
8
21
GLYCEROL (Link to PubChem not yet available)GLYCEROL
9
11
DODECYL-BETA-D-MALTOSIDE (Link to PubChem not yet available)DODECYL-BETA-D-MALTOSIDE
10
1
CA-MN4-O5 CLUSTER (Link to PubChem not yet available)CA-MN4-O5 CLUSTER
11
2
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)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
12
9
UNKNOWN LIGAND (Link to PubChem not yet available)UNKNOWN LIGAND
13
3
CALCIUM ION (Link to PubChem not yet available)CALCIUM ION
14
6
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE (Link to PubChem not yet available)1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
15
11
heptyl 1-thio-beta-D-glucopyranoside (Link to PubChem not yet available)heptyl 1-thio-beta-D-glucopyranoside
16
5
DIGALACTOSYL DIACYL GLYCEROL (DGDG) (Link to PubChem not yet available)DIGALACTOSYL DIACYL GLYCEROL (DGDG)
17
5
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE (Link to PubChem not yet available)1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
18
1
PROTOPORPHYRIN IX CONTAINING FE (Link to PubChem not yet available)PROTOPORPHYRIN IX CONTAINING FE
19
1
MAGNESIUM ION (Link to PubChem not yet available)MAGNESIUM ION
20
1
HEME C (Link to PubChem not yet available)HEME C
* 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