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Bacterial photosynthetic reaction center from rhodobacter sphaeroides with ile M265 replaced with ser

Analyse Bacterial photosynthetic reaction center from rhodobacter sphaeroides with ile… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4H9L
Type: protein
Length: 819 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Reaction center protein L chain; Reaction center protein M chain; Reaction center protein…
UniProt: P0C0Y8, P0C0Y9, P0C0Y7
Ligands: BCL, BPH, U10, SPO, FE
Pockets: 14 · best druggability 0.82

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Reaction center protein L chain	protein	280	63% helix, 4% strand	P0C0Y8
M	Reaction center protein M chain	protein	301	64% helix, 4% strand	P0C0Y9
H	Reaction center protein H chain	protein	238	24% helix, 24% strand	P0C0Y7

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
SPO · Spheroidene · 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

14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	792	0.82	0.84	70	BCL
2	114	0.78	0.97	32	empty
3	208	0.70	0.86	32	U10
4	55	0.67	0.95	19	empty
5	129	0.57	0.83	21	U10

Interfaces

3 interfaces between chains.

L–M · 4547 Å² buried · 63 hydrogen bonds · protein-protein
M–H · 2801 Å² buried · 37 hydrogen bonds · protein-protein
L–H · 1585 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

4H9L · Bacterial Photosynthetic Reaction Center from Rhodobacter sphaeroides with ILE M265… · 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 P0C0Y8
Every structure of UniProt P0C0Y9
Every structure of UniProt P0C0Y7
Elsewhere: RCSB PDB 4H9L · PDBe 4H9L · UniProt P0C0Y8 · UniProt P0C0Y9 · UniProt P0C0Y7

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