Research workbench

Crystal structure of integrin alpha V beta 3 with coil-coiled tag.

Analyse Crystal structure of integrin alpha V beta 3 with coil-coiled tag. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4G1E
Type: protein
Length: 1,673 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Integrin alpha-V; Integrin beta-3
UniProt: P06756, P05106
Ligands: NAG, MAN, BMA, CA, NI, CL, SO4
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 13% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Integrin alpha-V	protein	964	6% helix, 43% strand	P06756
B	Integrin beta-3	protein	709	23% helix, 27% strand	P05106

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 28 copies · chains A, B
MAN · alpha-D-mannopyranose · sugar · 12 copies · chains A, B
BMA · beta-D-mannopyranose · sugar · 9 copies · chains A, B
CA · Calcium ion · metal · 6 copies · chains A, B
NI · Nickel (II) ion · metal · chains A
CL · Chloride ion · ion · 7 copies · chains A, B
SO4 · Sulfate ion · ion · 6 copies · chains A, B

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

Pockets

20 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	867	0.81	0.83	100	NAG, MAN, SO4
2	606	0.79	0.85	54	CL
3	1098	0.78	0.80	80	NAG
4	776	0.73	0.78	63	empty
5	397	0.65	0.79	38	empty

Interfaces

1 interface between chains.

A–B · 4892 Å² buried · 38 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 38 disulfide, 15 glycan (disulfide, N-glycosylation).

Compared structures

4G1E · Crystal structure of integrin alpha V beta 3 with coil-coiled tag. · the same entry in another collection · chain A against A, TM-score 1.00
P06756 · AlphaFold monomer V2.0 prediction for integrin alpha-V (P06756) · a predicted model of the same protein · chain A against A, TM-score 0.93

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 P06756
Every structure of UniProt P05106
Elsewhere: RCSB PDB 4G1E · PDBe 4G1E · UniProt P06756 · UniProt P05106

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