MolNFT v1 · #11722 · protein
Crystal structure of the extracellular segment of integrin ALPHAVBETA3
1JV2 · Integrin, alpha V: “Crystal structure of the extracellular segment of integrin ALPHAVBETA3”. X-ray diffraction, 3 ligands (NAG, NDG, CA), 17 pockets (best druggability 0.80). MolNFT v1 #11722 on GenesisL1: 3D structure, binding…
- PDB
- 1JV2
- Type
- protein
- Length
- 1,466 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin, alpha V; Platelet membrane glycoprotein iiia beta subunit
- Ligands
- NAG, NDG, CA
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin, alpha V | protein | 927 | 3% helix, 39% strand | — |
| B | Platelet membrane glycoprotein iiia beta subunit | protein | 539 | 16% helix, 23% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A, B
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 3 copies · chains A, B
- CA · Calcium ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1042 | 0.80 | 0.82 | 98 | empty |
| 2 | 661 | 0.78 | 0.84 | 56 | empty |
| 3 | 599 | 0.68 | 0.77 | 49 | NAG |
| 4 | 86 | 0.51 | 0.83 | 24 | empty |
| 5 | 146 | 0.43 | 0.75 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 2960 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 25 disulfide, 11 glycan (disulfide, N-glycosylation).
Compared structures
- 1JV2 · Crystal structure of the extracellular segment of integrin ALPHAVBETA3 · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 1JV2 · PDBe 1JV2
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