Research workbench

Crystal structure of short hoefavidin biotin complex

Analyse Crystal structure of short hoefavidin biotin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4Z28
Type: protein
Length: 253 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Avidin family
UniProt: A9D857
Ligands: BTN
Pockets: 3 · best druggability 0.52

Structure

x-ray diffraction · 2 distinct chains · 5% helix, 61% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Avidin family	protein	127	6% helix, 61% strand	A9D857
B	Avidin family	protein	126	4% helix, 62% strand	A9D857

Ligands and binding sites

BTN · Biotin · ligand · 2 copies · chains A, B
BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B

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

Pockets

3 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	103	0.52	0.82	20	BTN
2	98	0.50	0.82	20	BTN
3	154	0.49	0.78	37	empty

Interfaces

1 interface between chains.

A–B · 1630 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

4Z28 · Crystal structure of short hoefavidin biotin complex · the same entry in another collection · chain A against A, TM-score 1.00
A9D857 · AlphaFold monomer V2.0 prediction for hoefavidin (A9D857) · a predicted model of the same protein · chain B 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 A9D857
Elsewhere: RCSB PDB 4Z28 · PDBe 4Z28 · UniProt A9D857

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