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X-ray high resolution structure of the photosynthetic reaction center from Rb. sphaeroides at pH 6.5 in the charge-separated state, 3rd dataset

Analyse X-ray high resolution structure of the photosynthetic reaction center from Rb.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2UWV
Type: protein
Length: 823 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.13
Source: RHODOBACTER SPHAEROIDES
Molecule: Reaction center protein H chain; Reaction center protein L chain; Reaction center protein…
UniProt: P0C0Y7, P0C0Y8, P0C0Y9
Ligands: BCL, BPH, UQ2, HTO, U10, SPO, FE, PO4
Pockets: 12 · best druggability 0.83

Structure

x-ray diffraction · resolution 2.13 · 3 distinct chains · 52% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Reaction center protein H chain	protein	240	25% helix, 25% strand	P0C0Y7
L	Reaction center protein L chain	protein	281	62% helix, 4% strand	P0C0Y8
M	Reaction center protein M chain	protein	302	64% helix, 4% strand	P0C0Y9

Ligands and binding sites

BCL · Bacteriochlorophyll A · ligand · 4 copies · chains L, M
BPH · Bacteriopheophytin A · ligand · 2 copies · chains L, M
UQ2 · Ubiquinone-2 · ligand · chains L, M
HTO · Heptane-1,2,3-triol · ligand · chains L
U10 · Ubiquinone-10 · ligand · chains L, M
SPO · Spheroidene · ligand · chains M
FE · Fe (III) ion · metal · chains L, M
PO4 · Phosphate ion · ion · chains L
LDA · Lauryl dimethylamine-N-oxide · additive · 8 copies · chains L, H, M
GOL · Glycerol · additive · 7 copies · chains H, L, M

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	903	0.83	0.85	84	BCL
2	112	0.78	0.97	32	empty
3	204	0.68	0.85	30	U10
4	219	0.63	0.83	38	empty
5	145	0.61	0.84	28	UQ2

Interfaces

3 interfaces between chains.

L–M · 4572 Å² buried · 65 hydrogen bonds · protein-protein
H–M · 2776 Å² buried · 43 hydrogen bonds · protein-protein
H–L · 1613 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

2UWV · X-ray high resolution structure of the photosynthetic reaction center from rb.… · the same entry in another collection · chain H against H, TM-score 1.00
P0C0Y8 · AlphaFold monomer V2.0 prediction for reaction center protein L chain (P0C0Y8) · a predicted model of the same protein · chain L against A, TM-score 1.00
P0C0Y9 · AlphaFold monomer V2.0 prediction for reaction center protein M chain (P0C0Y9) · a predicted model of the same protein · chain M against A, TM-score 0.99
P0C0Y7 · AlphaFold monomer V2.0 prediction for reaction center protein H chain (P0C0Y7) · a predicted model of the same protein · chain H against A, TM-score 0.98

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P0C0Y7
Every structure of UniProt P0C0Y8
Every structure of UniProt P0C0Y9
Elsewhere: RCSB PDB 2UWV · PDBe 2UWV · UniProt P0C0Y7 · UniProt P0C0Y8 · UniProt P0C0Y9

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