Research workbench
Integrin ALAPHIIBBETA3 complex with lotrafiban
Analyse Integrin ALAPHIIBBETA3 complex with lotrafiban in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UDG
- Type
- protein
- Length
- 2,702 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-iib heavy chain; Isoform beta-3C of integrin beta-3; 10E5 Fab heavy chain…
- UniProt
- P08514, P05106
- Ligands
- MWI, NAG, MAN, BMA, CA, MG, SO4, CL
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 7 distinct chains · 12% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-iib heavy chain | protein | 454 | 7% helix, 41% strand | P08514 |
| B | Isoform beta-3C of integrin beta-3 | protein | 466 | 23% helix, 29% strand | P05106 |
| C | Integrin alpha-iib heavy chain | protein | 453 | 6% helix, 39% strand | P08514 |
| D | Isoform beta-3C of integrin beta-3 | protein | 471 | 22% helix, 29% strand | P05106 |
| E | 10E5 Fab heavy chain | protein | 214 | 4% helix, 50% strand | — |
| F, L | 10E5 Fab light chain | protein | 214 | 5% helix, 50% strand | — |
| H | 10E5 Fab heavy chain | protein | 216 | 3% helix, 53% strand | — |
Ligands and binding sites
- MWI · Lotrafiban · ligand · 2 copies · chains A, B, C, D
- 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 · 10 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains B, D
- SO4 · Sulfate ion · ion · 9 copies · chains A, C, D, L
- CL · Chloride ion · ion · 3 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 660 | 0.79 | 0.84 | 52 | empty |
| 2 | 647 | 0.77 | 0.83 | 54 | empty |
| 3 | 954 | 0.76 | 0.78 | 62 | MWI |
| 4 | 573 | 0.74 | 0.82 | 62 | CL |
| 5 | 493 | 0.73 | 0.82 | 41 | empty |
Interfaces
12 interfaces between chains.
- E–F · 2106 Ų buried · 22 hydrogen bonds · protein-protein
- H–L · 2052 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1887 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1843 Ų buried · 25 hydrogen bonds · protein-protein
- C–E · 692 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 37 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 7UDG · Integrin alpha IIB beta3 complex with lotrafiban · the same entry in another collection · chain H against H, 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 7UDG · PDBe 7UDG · UniProt P08514 · UniProt P05106
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