MolNFT v1 · #18556 · protein

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

1PSS: “Crystallographic analyses of site-directed mutants of the photosynthetic reaction center from rhodobacter…”. X-ray diffraction, 5 ligands (BCL, BPH, U10), 13 pockets (best druggability 0.82). MolNFT v1 #18556 on GenesisL1: 3D…

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
Every structure of UniProt P02954
Every structure of UniProt P02953
Every structure of UniProt P11846
Elsewhere: RCSB PDB 1PSS · PDBe 1PSS · UniProt P02954 · UniProt P02953 · UniProt P11846

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