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Structure of the all-trans isomer of pharaonis halorhodopsin in the absence of halide ions

Analyse Structure of the all-trans isomer of pharaonis halorhodopsin in the absence of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5ETZ
Type: protein
Length: 781 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Halorhodopsin
UniProt: Q3ITX1
Ligands: L3P, BNG, RET, 22B
Pockets: 9 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 73% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Halorhodopsin	protein	261	72% helix, 5% strand	Q3ITX1
B, D	Halorhodopsin	protein	260	73% helix, 4% strand	Q3ITX1

Ligands and binding sites

L3P · 2,3-di-O-phytanly-3-sn-glycero-1-phosphoryl-3'-sn-glycerol-1'-phosphate · ligand · 6 copies · chains A, D, B
BNG · nonyl beta-D-glucopyranoside · ligand · 6 copies · chains A, D, B
RET · Retinal · ligand · 3 copies · chains A, B, D
22B · Bacterioruberin · ligand · chains A, B

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

Pockets

9 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	127	0.79	0.97	24	RET
2	123	0.79	0.97	24	RET
3	127	0.78	0.96	24	RET
4	575	0.72	0.79	52	22B, L3P
5	345	0.63	0.78	30	BNG

Interfaces

3 interfaces between chains.

A–D · 833 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 784 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 781 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 cofactor (retinal Schiff base).

Compared structures

5ETZ · Structure of the all-trans isomer of pharaonis halorhodopsin in the absence of halide ions · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

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Every structure of UniProt Q3ITX1
Elsewhere: RCSB PDB 5ETZ · PDBe 5ETZ · UniProt Q3ITX1

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