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Crystal structure of a blue-light absorbing proteorhodopsin mutant D97N from HOT75

Analyse Crystal structure of a blue-light absorbing proteorhodopsin mutant D97N from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4KLY
Type: protein
Length: 1,137 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Blue-light absorbing proteorhodopsin
UniProt: Q9AFF7
Ligands: RET
Pockets: 19 · best druggability 0.83

Structure

x-ray diffraction · 5 distinct chains · 82% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Blue-light absorbing proteorhodopsin	protein	228	82% helix, 0% strand	Q9AFF7
B	Blue-light absorbing proteorhodopsin	protein	232	82% helix, 0% strand	Q9AFF7
C	Blue-light absorbing proteorhodopsin	protein	230	83% helix, 0% strand	Q9AFF7
D	Blue-light absorbing proteorhodopsin	protein	221	83% helix, 0% strand	Q9AFF7
E	Blue-light absorbing proteorhodopsin	protein	226	81% helix, 0% strand	Q9AFF7

Ligands and binding sites

RET · Retinal · ligand · 5 copies · chains A, B, C, D, E

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	150	0.83	0.98	21	RET
2	137	0.82	0.98	22	RET
3	139	0.82	0.98	22	RET
4	136	0.81	0.98	24	RET
5	118	0.80	0.98	23	RET

Interfaces

5 interfaces between chains.

D–E · 897 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 880 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 879 Å² buried · 15 hydrogen bonds · protein-protein
A–E · 860 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 856 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 50 modified, 5 cofactor (engineered, retinal Schiff base).

Compared structures

4KLY · Crystal structure of a blue-light absorbing proteorhodopsin mutant D97N from HOT75 · the same entry in another collection · chain E against E, TM-score 1.00
Q9AFF7 · AlphaFold monomer V2.0 prediction for blue-light absorbing proteorhodopsin (Q9AFF7) · a predicted model of the same protein · chain D against A, TM-score 0.98

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 Q9AFF7
Elsewhere: RCSB PDB 4KLY · PDBe 4KLY · UniProt Q9AFF7

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