MolNFT v1 · #188869 · protein
Integrin ALAPHIIBBETA3 complex with UR2922 in MN2+
7UJE · Integrin alpha-iib: “Integrin ALAPHIIBBETA3 complex with UR2922 in MN2+”. X-ray diffraction, 8 ligands (I1F, NAG, MAN), 20 pockets (best druggability 0.78). MolNFT v1 #188869 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7UJE
- Type
- protein
- Length
- 2,702 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-iib; Integrin beta-3; Fab heavy chain; Fab light chain
- UniProt
- P08514, P05106
- Ligands
- I1F, NAG, MAN, BMA, CA, MN, SO4, CL
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 7 distinct chains · 12% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-iib | protein | 454 | 6% helix, 41% strand | P08514 |
| B | Integrin beta-3 | protein | 466 | 23% helix, 30% strand | P05106 |
| C | Integrin alpha-iib | protein | 453 | 7% helix, 41% strand | P08514 |
| D | Integrin beta-3 | protein | 471 | 23% helix, 28% strand | P05106 |
| E | Fab heavy chain | protein | 214 | 4% helix, 50% strand | — |
| F, L | Fab light chain | protein | 214 | 5% helix, 51% strand | — |
| H | Fab heavy chain | protein | 216 | 3% helix, 51% strand | — |
Ligands and binding sites
- I1F · {5-[N-(4-carbamimidoylbenzoyl)-4-nitro-L-phenylalanyl]-4,5,6,7-tetrahydro-2H-pyrazolo[4,3-c]pyridin-2-yl}acetic acid · 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 · 4 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, D
- SO4 · Sulfate ion · ion · 9 copies · chains A, C, D, L
- CL · Chloride ion · ion · 3 copies · chains C, D
- 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 658 | 0.78 | 0.83 | 53 | empty |
| 2 | 671 | 0.78 | 0.83 | 56 | empty |
| 3 | 821 | 0.74 | 0.78 | 62 | empty |
| 4 | 742 | 0.73 | 0.79 | 60 | empty |
| 5 | 537 | 0.73 | 0.81 | 56 | CL |
Interfaces
12 interfaces between chains.
- E–F · 2068 Ų buried · 18 hydrogen bonds · protein-protein
- H–L · 2044 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1813 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1805 Ų buried · 21 hydrogen bonds · protein-protein
- C–E · 633 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 37 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 7UJE · Integrin alpha IIB beta3 complex with UR2922 in Mn2+ · 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 7UJE · PDBe 7UJE · UniProt P08514 · UniProt P05106
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