MolNFT v1 · #161146 · protein

Crystal structure of the light-harvesting complex II (B800-850) from ectothiorhodospira haloalkaliphila

6Q53 · Light-harvesting protein subunit alpha: “Crystal structure of the light-harvesting complex II (B800-850) from ectothiorhodospira haloalkaliphila”. X-ray diffraction, 3 ligands (BCL, DET, LYC), 3 pockets (best druggability 0.66).…

PDB: 6Q53
Type: protein
Length: 197 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Light-harvesting protein subunit alpha; Light-harvesting protein B:800-850 subunit beta
UniProt: W8L932
Ligands: BCL, DET, LYC
Pockets: 3 · best druggability 0.66

Structure

x-ray diffraction · 3 distinct chains · 63% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Light-harvesting protein subunit alpha	protein	54	65% helix, 0% strand	—
B, E	Light-harvesting protein B:800-850 subunit beta	protein	43	74% helix, 0% strand	W8L932
D	Light-harvesting protein subunit alpha	protein	57	53% helix, 0% strand	—

Ligands and binding sites

BCL · Bacteriochlorophyll A · ligand · 6 copies · chains A, B, E, D
DET · Undecylamine-N,N-dimethyl-N-oxide · ligand · 3 copies · chains B, E
LYC · Lycopene · ligand · 2 copies · chains A, B, D, E

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	473	0.66	0.77	37	LYC
2	229	0.50	0.74	27	empty
3	125	0.38	0.73	13	empty

Interfaces

6 interfaces between chains.

A–B · 718 Å² buried · 10 hydrogen bonds · protein-protein
D–E · 686 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 652 Å² buried · 3 hydrogen bonds · protein-protein
A–E · 426 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 176 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6Q53 · CRYSTAL STRUCTURE OF THE LIGHT-HARVESTING COMPLEX II (B800-850) FROM Ectothiorhodospira… · the same entry in another collection · chain A against A, 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 W8L932
Elsewhere: RCSB PDB 6Q53 · PDBe 6Q53 · UniProt W8L932

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