Research workbench
Structural basis for allostery in integrins and binding of ligand- mimetic therapeutics to the platelet receptor for fibrinogen
Analyse Structural basis for allostery in integrins and binding of ligand- mimetic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TYE
- Type
- protein
- Length
- 2,676 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-iib; Integrin beta-3
- UniProt
- P08514, P05106
- Ligands
- NAG, MAN, BMA, CA, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Integrin alpha-iib | protein | 452 | 6% helix, 40% strand | P08514 |
| B, D, F | Integrin beta-3 | protein | 440 | 25% helix, 27% strand | P05106 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B, C, D, E, F
- MAN · alpha-D-mannopyranose · sugar · 4 copies
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A, E
- CA · Calcium ion · metal · 18 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 3 copies · chains B, D, F
- CAC · Cacodylate ion · additive · 3 copies · chains B, D, 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 854 | 0.83 | 0.86 | 85 | empty |
| 2 | 1064 | 0.80 | 0.82 | 87 | empty |
| 3 | 700 | 0.78 | 0.82 | 58 | empty |
| 4 | 689 | 0.77 | 0.82 | 53 | empty |
| 5 | 650 | 0.77 | 0.82 | 53 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1729 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1725 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1716 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 794 Ų buried · 14 hydrogen bonds · protein-protein
- C–E · 719 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 33 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 1TYE · Structural basis for allostery in integrins and binding of ligand-mimetic therapeutics to… · the same entry in another collection · chain B against B, 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 0.99
- P05106 · AlphaFold monomer V2.0 prediction for integrin beta-3 (P05106) · a predicted model of the same protein · chain B 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 1TYE · PDBe 1TYE · UniProt P08514 · UniProt P05106
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