Research workbench

Crystal structure of monoac-biotin-avidin complex

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

PDB: 3VGW
Type: protein
Length: 976 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Avidin
UniProt: P02701
Ligands: NVZ, NAG, SO4
Pockets: 10 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G	Avidin	protein	123	7% helix, 50% strand	P02701
B, D, F, H	Avidin	protein	121	7% helix, 50% strand	P02701

Ligands and binding sites

NVZ · 5-[(3aS,4S,6aR)-1-acetyl-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid · ligand · 8 copies · chains A, C, B, D, E, G, F, H
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D, E, F, G, H
SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D, E, F, G, H

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	714	0.84	0.87	112	NVZ
2	197	0.75	0.90	39	NVZ
3	236	0.72	0.87	38	NVZ
4	134	0.72	0.91	24	NVZ
5	268	0.70	0.85	47	NVZ

Interfaces

18 interfaces between chains.

E–F · 1928 Å² buried · 36 hydrogen bonds · protein-protein
G–H · 1927 Å² buried · 37 hydrogen bonds · protein-protein
C–D · 1917 Å² buried · 35 hydrogen bonds · protein-protein
A–B · 1886 Å² buried · 33 hydrogen bonds · protein-protein
E–G · 632 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 8 glycan (disulfide, N-glycosylation).

Compared structures

3VGW · Crystal structure of monoAc-biotin-avidin complex · the same entry in another collection · chain H against H, TM-score 1.00
P02701 · AlphaFold monomer V2.0 prediction for avidin (P02701) · a predicted model of the same protein · chain A 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 P02701
Elsewhere: RCSB PDB 3VGW · PDBe 3VGW · UniProt P02701

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