Research workbench
Integrin alphaiib BETA3 headpiece and rgd peptide complex
Analyse Integrin alphaiib BETA3 headpiece and rgd peptide complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZDY
- Type
- protein
- Length
- 2,711 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-iib; Integrin beta-3; 10E5 Fab heavy chain; 10E5 Fab light chain; Rgd…
- UniProt
- P08514, P05106
- Ligands
- NAG, BMA, MAN, CA, MG, SO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 8 distinct chains · 13% 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 | 464 | 22% helix, 30% strand | P05106 |
| C | Integrin alpha-iib | protein | 453 | 6% helix, 41% strand | P08514 |
| D | Integrin beta-3 | protein | 469 | 24% helix, 29% strand | P05106 |
| E, H | 10E5 Fab heavy chain | protein | 216 | 6% helix, 50% strand | — |
| F, L | 10E5 Fab light chain | protein | 214 | 4% helix, 53% strand | — |
| I | Rgd peptide | protein | 6 | 0% helix, 17% strand | — |
| J | Rgd peptide | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, C
- CA · Calcium ion · metal · 12 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains B, I, D, J
- SO4 · Sulfate ion · ion · 20 copies · chains A, H, B, C, E, D, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 706 | 0.79 | 0.83 | 52 | empty |
| 2 | 709 | 0.78 | 0.83 | 55 | empty |
| 3 | 1162 | 0.77 | 0.79 | 87 | SO4, MG, CA |
| 4 | 802 | 0.77 | 0.81 | 73 | SO4 |
| 5 | 592 | 0.74 | 0.81 | 59 | SO4 |
Interfaces
16 interfaces between chains.
- H–L · 1998 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1960 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1826 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1818 Ų buried · 20 hydrogen bonds · protein-protein
- C–E · 683 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 37 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
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 3ZDY · PDBe 3ZDY · UniProt P08514 · UniProt P05106
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