MolNFT v1 · #28144 · protein

Structure of insect cell (baculovirus) expressed AVR4 (C122S)-biotin complex

1Y52 · Avidin-related protein 4/5: “Structure of insect cell (baculovirus) expressed AVR4 (C122S)-biotin complex”. X-ray diffraction, 2 ligands (BTN, NAG), 2 pockets (best druggability 0.57). MolNFT v1 #28144 on GenesisL1: 3D structure…

PDB: 1Y52
Type: protein
Length: 240 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Avidin-related protein 4/5
UniProt: P56734
Ligands: BTN, NAG
Pockets: 2 · best druggability 0.57

Structure

x-ray diffraction · 1 distinct chain · 8% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
X, Y	Avidin-related protein 4/5	protein	120	8% helix, 50% strand	P56734

Ligands and binding sites

BTN · Biotin · ligand · 2 copies · chains X, Y
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains X, Y

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	126	0.57	0.83	20	BTN
2	125	0.56	0.83	20	BTN

Interfaces

1 interface between chains.

X–Y · 1740 Å² buried · 23 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 glycan, 2 disulfide (N-glycosylation, disulfide).

Compared structures

1Y52 · structure of insect cell (Baculovirus) expressed AVR4 (C122S)-biotin complex · the same entry in another collection · chain X against X, TM-score 1.00
P56734 · AlphaFold monomer V2.0 prediction for avidin-related protein 4/5 (P56734) · a predicted model of the same protein · chain X against A, TM-score 0.99

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 P56734
Elsewhere: RCSB PDB 1Y52 · PDBe 1Y52 · UniProt P56734

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.