Research workbench
Integrin ALPHAIIBBETA3 in complex with agdv-NH2 peptide
Analyse Integrin ALPHAIIBBETA3 in complex with agdv-NH2 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Z7Q
- Type
- protein
- Length
- 2,710 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-iib; Integrin beta-3; Monoclonal antibody 10E5 heavy chain; Monoclonal…
- UniProt
- P08514, P05106
- Ligands
- NAG, MAN, BMA, CA, MN, SO4, NH2, CL
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 8 distinct chains · 11% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-iib | protein | 454 | 5% helix, 39% strand | P08514 |
| B | Integrin beta-3 | protein | 466 | 23% helix, 30% strand | P05106 |
| C | Integrin alpha-iib | protein | 453 | 5% helix, 40% strand | P08514 |
| D | Integrin beta-3 | protein | 471 | 22% helix, 29% strand | P05106 |
| E | Monoclonal antibody 10E5 heavy chain | protein | 214 | 4% helix, 50% strand | — |
| F, L | Monoclonal antibody 10E5 light chain | protein | 214 | 4% helix, 47% strand | — |
| H | Monoclonal antibody 10E5 heavy chain | protein | 216 | 3% helix, 52% strand | — |
| G, I | Tetrapeptide agdv-NH2 | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A, C
- BMA · beta-D-mannopyranose · sugar · 2 copies
- CA · Calcium ion · metal · 8 copies · chains A, C
- MN · Manganese (II) ion · metal · 6 copies · chains B, G, D, I
- SO4 · Sulfate ion · ion · 7 copies · chains A, C, D, L
- NH2 · Amino group · ion · 2 copies · chains B, G, D, I
- CL · Chloride ion · ion · chains C
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 667 | 0.79 | 0.84 | 55 | empty |
| 2 | 804 | 0.78 | 0.81 | 57 | NH2, MN |
| 3 | 657 | 0.77 | 0.83 | 56 | empty |
| 4 | 642 | 0.75 | 0.81 | 47 | SO4 |
| 5 | 577 | 0.73 | 0.81 | 60 | empty |
Interfaces
16 interfaces between chains.
- E–F · 2081 Ų buried · 15 hydrogen bonds · protein-protein
- H–L · 2068 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1863 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1833 Ų buried · 23 hydrogen bonds · protein-protein
- C–E · 669 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 37 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 4Z7Q · Integrin alphaIIbbeta3 in complex with AGDV-NH2 peptide · 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
- Every structure of UniProt P08514
- Every structure of UniProt P05106
- Elsewhere: RCSB PDB 4Z7Q · PDBe 4Z7Q · UniProt P08514 · UniProt P05106
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.