Research workbench

Integrin ALPHAVBETA3 ectodomain bound to the tenth domain of fibronectin with the iakgdwnd motif

Analyse Integrin ALPHAVBETA3 ectodomain bound to the tenth domain of fibronectin with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4MMY
Type: protein
Length: 1,622 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Integrin alpha-V; Integrin beta-3; Fibronectin
UniProt: P06756, P05106, P02751
Ligands: NAG, BMA, MAN, MN
Pockets: 18 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 8% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Integrin alpha-V	protein	924	2% helix, 46% strand	P06756
B	Integrin beta-3	protein	690	17% helix, 25% strand	P05106
C	Fibronectin	protein	8	0% helix, 0% strand	P02751

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 23 copies · chains A, B
BMA · beta-D-mannopyranose · sugar · 6 copies · chains A
MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A
MN · Manganese (II) ion · metal · 8 copies · chains A, B, C

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

Pockets

18 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	681	0.77	0.82	67	empty
2	580	0.76	0.83	56	empty
3	1113	0.71	0.75	88	empty
4	802	0.71	0.77	80	empty
5	492	0.65	0.77	51	empty

Interfaces

3 interfaces between chains.

A–B · 3484 Å² buried · 29 hydrogen bonds · protein-protein
B–C · 345 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 172 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 37 disulfide, 14 glycan (disulfide, N-glycosylation).

Compared structures

P06756 · AlphaFold monomer V2.0 prediction for integrin alpha-V (P06756) · a predicted model of the same protein · chain A against A, TM-score 0.98
P02751 · AlphaFold monomer V2.0 prediction for fibronectin (P02751) · a predicted model of the same protein · chain C against A, TM-score 0.49

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
Every structure of UniProt P02751
Elsewhere: RCSB PDB 4MMY · PDBe 4MMY · UniProt P06756 · UniProt P05106 · UniProt P02751

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