MolNFT v1 · #107760 · protein

Crystal structure of alpha V beta 6 with peptide

4UM9 · Integrin alpha-V: “Crystal structure of alpha V beta 6 with peptide”. X-ray diffraction, 8 ligands (ACE, NAG, MAN), 20 pockets (best druggability 0.81). MolNFT v1 #107760 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4UM9
Type: protein
Length: 2,107 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Integrin alpha-V; Integrin beta-6; Transforming growth factor beta 3
UniProt: P06756, P18564, Q6TV15
Ligands: ACE, NAG, MAN, BMA, CA, MG, SO4, NHH
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 6 distinct chains · 13% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Integrin alpha-V	protein	594	4% helix, 43% strand	P06756
B	Integrin beta-6	protein	448	24% helix, 28% strand	P18564
C	Integrin alpha-V	protein	589	5% helix, 44% strand	P06756
D	Integrin beta-6	protein	455	24% helix, 28% strand	P18564
E	Transforming growth factor beta 3	protein	10	40% helix, 0% strand	Q6TV15
F	Transforming growth factor beta 3	protein	11	36% helix, 0% strand	Q6TV15

Ligands and binding sites

ACE · Acetyl group · ligand · chains D, F
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 28 copies · chains A, C, B, D
MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A, C
BMA · beta-D-mannopyranose · sugar · 4 copies · chains C
CA · Calcium ion · metal · 12 copies · chains A, B, C, D, F
MG · Magnesium ion · metal · 2 copies · chains B, E, D, F
SO4 · Sulfate ion · ion · 6 copies · chains A, B, C
NHH · N'-{4-[2-(diaminomethylidene) hydrazono]cyclohexyliden}aminomethanehydrazonamide · ion · 2 copies · chains D, E, F

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	653	0.81	0.86	60	empty
2	668	0.80	0.84	62	empty
3	535	0.66	0.77	64	empty
4	654	0.65	0.75	73	SO4
5	280	0.65	0.82	42	ACE, CA

Interfaces

9 interfaces between chains.

C–D · 2017 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 2002 Å² buried · 27 hydrogen bonds · protein-protein
B–D · 686 Å² buried · 1 hydrogen bond · protein-protein
D–F · 499 Å² buried · 7 hydrogen bonds · protein-protein
B–E · 424 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 34 disulfide, 18 glycan, 1 covalent (disulfide, N-glycosylation, covalent ligand).

Compared structures

P06756 · AlphaFold monomer V2.0 prediction for integrin alpha-V (P06756) · a predicted model of the same protein · chain C against A, TM-score 0.99
P18564 · AlphaFold monomer V2.0 prediction for integrin beta-6 (P18564) · a predicted model of the same protein · chain D 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 P06756
Every structure of UniProt P18564
Every structure of UniProt Q6TV15
Elsewhere: RCSB PDB 4UM9 · PDBe 4UM9 · UniProt P06756 · UniProt P18564 · UniProt Q6TV15

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