MolNFT v1 · #87755 · protein
Three-dimensional reconstruction of intact human integrin ALPHAIIBBETA3 in a phospholipid bilayer nanodisc
4CAK · Integrin alpha-iib: “Three-dimensional reconstruction of intact human integrin ALPHAIIBBETA3 in a phospholipid bilayer nanodisc”. Electron microscopy, 3 ligands (NAG, BMA, MAN), 19 pockets (best druggability 0.81). MolNFT v1 #87755…
- PDB
- 4CAK
- Type
- protein
- Length
- 1,592 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-iib; Integrin beta-3
- UniProt
- P08514, P05106
- Ligands
- NAG, BMA, MAN
- Pockets
- 19 · best druggability 0.81
Structure
electron microscopy · 2 distinct chains · 9% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-iib | protein | 912 | 3% helix, 48% strand | P08514 |
| B | Integrin beta-3 | protein | 680 | 16% helix, 28% strand | P05106 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains B, A
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 975 | 0.81 | 0.82 | 108 | NAG |
| 2 | 1144 | 0.81 | 0.82 | 97 | empty |
| 3 | 286 | 0.67 | 0.82 | 39 | empty |
| 4 | 324 | 0.54 | 0.74 | 37 | empty |
| 5 | 114 | 0.51 | 0.81 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 5974 Ų buried · 501 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 33 disulfide, 33 glycan, 6 isopeptide (disulfide, glycosylation, isopeptide, N-glycosylation, O-glycosylation).
Compared structures
- 4CAK · Three-dimensional reconstruction of intact human integrin alphaIIbbeta3 in a phospholipid… · the same entry in another collection · chain A against A, TM-score 1.00
- P08514 · AlphaFold monomer V2.0 prediction for integrin alpha-iib (P08514) · a predicted model of the same protein · chain A against A, TM-score 0.57
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 4CAK · PDBe 4CAK · UniProt P08514 · UniProt P05106
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