MolNFT v1 · #72769 · protein
The closed headpiece of integrin alphaiib BETA3 and its complex with an alpahiib BETA3 -specific antagonist that does not induce opening
3NID · Integrin alpha-iib: “The closed headpiece of integrin alphaiib BETA3 and its complex with an alpahiib BETA3 -specific antagonist…”. X-ray diffraction, 5 ligands (NAG, MAN, CA), 20 pockets (best druggability 0.80). MolNFT v1 #72769…
- PDB
- 3NID
- 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
- NAG, MAN, CA, MG, SO4
- Pockets
- 20 · best druggability 0.80
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, 29% strand | P05106 |
| C | Integrin alpha-iib | protein | 453 | 6% helix, 40% strand | P08514 |
| D | Integrin beta-3 | protein | 471 | 23% helix, 29% strand | P05106 |
| E | Monoclonal antibody 10E5 heavy chain | protein | 214 | 4% helix, 52% strand | — |
| F, L | Monoclonal antibody 10E5 light chain | protein | 214 | 6% helix, 48% strand | — |
| H | Monoclonal antibody 10E5 heavy chain | protein | 216 | 4% helix, 53% strand | — |
Ligands and binding sites
- 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
- CA · Calcium ion · metal · 12 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains B, D
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, D, H, L
- GOL · Glycerol · additive · 9 copies · chains A, 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 681 | 0.80 | 0.84 | 51 | empty |
| 2 | 640 | 0.77 | 0.83 | 55 | empty |
| 3 | 950 | 0.76 | 0.79 | 69 | GOL, MG |
| 4 | 711 | 0.76 | 0.81 | 51 | SO4 |
| 5 | 721 | 0.75 | 0.80 | 61 | empty |
Interfaces
12 interfaces between chains.
- E–F · 2081 Ų buried · 18 hydrogen bonds · protein-protein
- H–L · 1994 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1842 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1823 Ų buried · 23 hydrogen bonds · protein-protein
- C–E · 661 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 37 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 3NID · The Closed Headpiece of Integrin alphaIIB beta3 and its Complex with an alpahIIB beta3… · 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 3NID · PDBe 3NID · UniProt P08514 · UniProt P05106
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