MolNFT v1 · #51593 · protein
Re-refinement of integrin ALPHAIIBBETA3 headpiece bound to antagonist L-739758
2VC2 · Integrin alpha-iib: “Re-refinement of integrin ALPHAIIBBETA3 headpiece bound to antagonist L-739758”. X-ray diffraction, 5 ligands (180, MAN, NAG), 15 pockets (best druggability 0.77). MolNFT v1 #51593 on GenesisL1: 3D structure…
- PDB
- 2VC2
- Type
- protein
- Length
- 1,342 residues
- Chains
- 4
- 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
- 180, MAN, NAG, CA, MG
- Pockets
- 15 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-iib | protein | 452 | 7% helix, 44% strand | P08514 |
| B | Integrin beta-3 | protein | 457 | 23% helix, 28% strand | P05106 |
| H | Monoclonal antibody 10E5 heavy chain | protein | 219 | 7% helix, 51% strand | — |
| L | Monoclonal antibody 10E5 light chain | protein | 214 | 6% helix, 53% strand | — |
Ligands and binding sites
- 180 · 2-(S)-[N-(3-pyridylsulfonyl)amino]-3-[[2-carbonyl-5-[2-(piperidin-4-yl)ethyl]-thieno[2,3-b]thiopheneyl]amino]-propionic acid · ligand · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B
- CA · Calcium ion · metal · 6 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 667 | 0.77 | 0.83 | 52 | empty |
| 2 | 672 | 0.75 | 0.81 | 62 | empty |
| 3 | 190 | 0.54 | 0.78 | 32 | GOL |
| 4 | 264 | 0.50 | 0.74 | 35 | MG, 180 |
| 5 | 200 | 0.46 | 0.74 | 33 | empty |
Interfaces
4 interfaces between chains.
- H–L · 2024 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1721 Ų buried · 22 hydrogen bonds · protein-protein
- A–H · 627 Ų buried · 9 hydrogen bonds · protein-protein
- A–L · 404 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 2VC2 · Re-refinement of Integrin AlphaIIbBeta3 Headpiece Bound to Antagonist L-739758 · the same entry in another collection · chain A against A, 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 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 2VC2 · PDBe 2VC2 · UniProt P08514 · UniProt P05106
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