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Photosynthetic reaction center from R. sphaeroides analyzed at room temperature on an X-ray transparent microfluidic chip

Analyse Photosynthetic reaction center from R. sphaeroides analyzed at room temperature… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4TQQ
Type: protein
Length: 823 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Reaction center protein H chain; Reaction center protein L chain; Reaction center protein…
UniProt: P0C0Y7, P0C0Y8, P0C0Y9
Ligands: BCL, BPH, UQ1, U10, FE2
Pockets: 15 · best druggability 0.80

Structure

x-ray diffraction · 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, 24% strand	P0C0Y7
L	Reaction center protein L chain	protein	281	63% 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
UQ1 · Ubiquinone-1 · ligand · chains L
U10 · Ubiquinone-10 · ligand · chains H, L, M
FE2 · Fe (II) ion · metal · chains L, M

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

Pockets

15 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	735	0.80	0.84	55	BCL
2	223	0.75	0.89	34	U10
3	100	0.75	0.96	29	empty
4	57	0.70	0.97	16	empty
5	159	0.64	0.85	29	UQ1

Interfaces

3 interfaces between chains.

L–M · 4626 Å² buried · 64 hydrogen bonds · protein-protein
H–M · 2872 Å² buried · 37 hydrogen bonds · protein-protein
H–L · 1591 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

4TQQ · Photosynthetic Reaction Center from R. sphaeroides Analyzed at Room Temperature on an… · the same entry in another collection · chain H against H, TM-score 1.00

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 4TQQ · PDBe 4TQQ · UniProt P0C0Y7 · UniProt P0C0Y8 · UniProt P0C0Y9

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