Research workbench
Integrin ALPHAVBETA3 ectodomain bound to antagonist tdi-4161
Analyse Integrin ALPHAVBETA3 ectodomain bound to antagonist tdi-4161 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MK0
- Type
- protein
- Length
- 1,607 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
- JUY, NAG, BMA, MAN, MN
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-V | protein | 920 | 3% helix, 44% strand | P06756 |
| B | Integrin beta-3 | protein | 687 | 16% helix, 25% strand | P05106 |
Ligands and binding sites
- JUY · (2S)-2-[(1,3-benzothiazole-2-carbonyl)amino]-4-{[5-(1, 8-naphthyridin-2-yl)pentanoyl]amino}butanoic acid · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
- MN · Manganese (II) ion · metal · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 815 | 0.80 | 0.83 | 87 | empty |
| 2 | 647 | 0.77 | 0.82 | 58 | empty |
| 3 | 627 | 0.75 | 0.81 | 64 | empty |
| 4 | 434 | 0.73 | 0.83 | 44 | empty |
| 5 | 182 | 0.67 | 0.86 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 3462 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 37 disulfide, 14 glycan (disulfide, N-glycosylation).
Compared structures
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 6MK0 · PDBe 6MK0 · UniProt P06756 · UniProt P05106
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