MolNFT v1 · #81112 · protein

Crystal structure of visual arrestin

3UGX · S-arrestin: “Crystal structure of visual arrestin”. X-ray diffraction, 3 ligands (PTD, NA, K), 8 pockets (best druggability 0.73). MolNFT v1 #81112 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3UGX
Type: protein
Length: 1,427 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: S-arrestin
UniProt: P08168
Ligands: PTD, NA, K
Pockets: 8 · best druggability 0.73

Structure

x-ray diffraction · 4 distinct chains · 6% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	S-arrestin	protein	369	7% helix, 48% strand	P08168
B	S-arrestin	protein	352	5% helix, 52% strand	P08168
C	S-arrestin	protein	358	6% helix, 52% strand	P08168
D	S-arrestin	protein	348	6% helix, 54% strand	P08168

Ligands and binding sites

PTD · Pentanedial · ligand · 14 copies · chains A, B, C, D
NA · Sodium ion · metal · 2 copies · chains A, B
K · Potassium ion · metal · chains C, D
EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, C, D
IMD · Imidazole · additive · 3 copies · chains B, D

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

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	903	0.73	0.77	104	IMD, PTD
2	826	0.71	0.77	104	IMD
3	124	0.51	0.81	23	empty
4	145	0.50	0.79	27	empty
5	169	0.41	0.73	34	K, EDO

Interfaces

4 interfaces between chains.

A–D · 874 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 617 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 606 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 592 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

3UGX · Crystal Structure of Visual Arrestin · the same entry in another collection · chain D against D, TM-score 1.00
P08168 · AlphaFold monomer V2.0 prediction for S-arrestin (P08168) · a predicted model of the same protein · chain D against A, TM-score 0.95

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 P08168
Elsewhere: RCSB PDB 3UGX · PDBe 3UGX · UniProt P08168

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