Research workbench
A novel high affinity integrin ALPHAIIBBETA3 receptor antagonist that unexpectedly displaces MG2+ from the BETA3 midas
Analyse A novel high affinity integrin ALPHAIIBBETA3 receptor antagonist that… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3T3M
- 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; Monoclonal antibody 10E5 heavy chain; Monoclonal…
- UniProt
- P08514, P05106
- Ligands
- RC2, NAG, MAN, BMA, CA, SO4, CL
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 7 distinct chains · 12% helix, 38% 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, 29% strand | P05106 |
| C | Integrin alpha-iib | protein | 453 | 6% helix, 40% strand | P08514 |
| D | Integrin beta-3 | protein | 471 | 23% helix, 28% strand | P05106 |
| E | Monoclonal antibody 10E5 heavy chain | protein | 214 | 3% helix, 47% strand | — |
| F, L | Monoclonal antibody 10E5 light chain | protein | 214 | 6% helix, 45% strand | — |
| H | Monoclonal antibody 10E5 heavy chain | protein | 216 | 4% helix, 53% strand | — |
Ligands and binding sites
- RC2 · N-{3-[5-oxo-7-(piperazin-1-yl)-5H-[1,3,4]thiadiazolo[3,2-a]pyrimidin-2-yl]phenyl}glycinamide · 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 · 12 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, L
- CL · Chloride ion · ion · 3 copies · chains B, 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 733 | 0.79 | 0.83 | 55 | empty |
| 2 | 660 | 0.78 | 0.83 | 55 | empty |
| 3 | 729 | 0.76 | 0.81 | 65 | empty |
| 4 | 883 | 0.75 | 0.79 | 62 | RC2, CL |
| 5 | 717 | 0.74 | 0.80 | 55 | empty |
Interfaces
11 interfaces between chains.
- E–F · 2002 Ų buried · 18 hydrogen bonds · protein-protein
- H–L · 1949 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1806 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1796 Ų buried · 22 hydrogen bonds · protein-protein
- C–E · 658 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 37 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 3T3M · A Novel High Affinity Integrin alphaIIbbeta3 Receptor Antagonist That Unexpectedly… · the same entry in another collection · chain L against L, TM-score 1.00
- P08514 · AlphaFold monomer V2.0 prediction for integrin alpha-iib (P08514) · a predicted model of the same protein · chain C 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 3T3M · PDBe 3T3M · UniProt P08514 · UniProt P05106
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