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Crystallographic analyses of site-directed mutants of the photosynthetic reaction center from rhodobacter sphaeroides

Analyse Crystallographic analyses of site-directed mutants of the photosynthetic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1PST
Type: protein
Length: 799 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Photosynthetic reaction center
UniProt: P02954, P02953, P11846
Ligands: BCL, BPH, U10, CRT, FE
Pockets: 13 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 51% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Photosynthetic reaction center	protein	266	65% helix, 3% strand	P02954
M	Photosynthetic reaction center	protein	296	62% helix, 1% strand	P02953
H	Photosynthetic reaction center	protein	237	23% helix, 24% strand	P11846

Ligands and binding sites

BCL · Bacteriochlorophyll A · ligand · 3 copies · chains L, M
BPH · Bacteriopheophytin A · ligand · 3 copies · chains L, M
U10 · Ubiquinone-10 · ligand · 2 copies · chains L, M
CRT · Spirilloxanthin · ligand · chains M
FE · Fe (III) ion · metal · chains L, M

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

Pockets

13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	861	0.82	0.84	71	BCL, BPH
2	594	0.72	0.80	65	empty
3	222	0.68	0.84	29	U10
4	316	0.65	0.81	38	empty
5	122	0.64	0.88	29	empty

Interfaces

3 interfaces between chains.

L–M · 4121 Å² buried · 50 hydrogen bonds · protein-protein
M–H · 2600 Å² buried · 34 hydrogen bonds · protein-protein
L–H · 1417 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

1PST · Crystallographic analyses of site-directed mutants of the photosynthetic reaction center… · the same entry in another collection · chain L against L, TM-score 1.00

Analyse

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Elsewhere: RCSB PDB 1PST · PDBe 1PST · UniProt P02954 · UniProt P02953 · UniProt P11846

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