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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: 1PSS
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 · 52% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Photosynthetic reaction center	protein	266	68% helix, 3% strand	P02954
M	Photosynthetic reaction center	protein	296	61% helix, 3% strand	P02953
H	Photosynthetic reaction center	protein	237	21% helix, 20% strand	P11846

Ligands and binding sites

BCL · Bacteriochlorophyll A · ligand · 4 copies · chains L, M
BPH · Bacteriopheophytin A · ligand · 2 copies · chains L, M
U10 · Ubiquinone-10 · ligand · 2 copies · chains L, M, H
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, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	907	0.82	0.84	73	BCL
2	657	0.73	0.80	81	empty
3	311	0.70	0.84	52	empty
4	150	0.66	0.87	26	U10
5	146	0.65	0.86	25	U10

Interfaces

3 interfaces between chains.

L–M · 4165 Å² buried · 54 hydrogen bonds · protein-protein
M–H · 2547 Å² buried · 37 hydrogen bonds · protein-protein
L–H · 1404 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

1PSS · 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

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
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Elsewhere: RCSB PDB 1PSS · PDBe 1PSS · UniProt P02954 · UniProt P02953 · UniProt P11846

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