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Crystal structure of proton pump mar rhodopsin pressurized with krypton

Analyse Crystal structure of proton pump mar rhodopsin pressurized with krypton in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7Q37
Type: protein
Length: 217 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bacteriorhodopsin
UniProt: S5DM51
Ligands: LFA, RET, KR
Pockets: 2 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 84% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bacteriorhodopsin	protein	217	84% helix, 0% strand	S5DM51

Ligands and binding sites

LFA · Eicosane · ligand · 14 copies · chains A
RET · Retinal · ligand · chains A
KR · Krypton · ion · 19 copies · chains A
HEX · Hexane · additive · 5 copies · chains A

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

Pockets

2 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	138	0.81	0.97	21	RET
2	85	0.48	0.82	19	KR

Modifications

Observed in the structure: 1 cofactor, 1 modified (retinal Schiff base, formylation).

Compared structures

7Q37 · Crystal structure of proton pump MAR rhodopsin pressurized with krypton · 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 S5DM51
Elsewhere: RCSB PDB 7Q37 · PDBe 7Q37 · UniProt S5DM51

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