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
- 3ZE2
- Type
- protein
- Length
- 2,615 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, MAN, BMA, CA, MN, SO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 7 distinct chains · 13% 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 | 469 | 24% helix, 29% strand | P05106 |
| C | Integrin alpha-iib | protein | 453 | 6% helix, 41% strand | P08514 |
| D | Integrin beta-3 | protein | 367 | 25% helix, 32% strand | P05106 |
| E, H | 10E5 Fab heavy chain | protein | 216 | 8% helix, 53% strand | — |
| F, L | 10E5 Fab light chain | protein | 214 | 6% helix, 51% strand | — |
| I, J | Rgd peptide | protein | 6 | 0% helix, 17% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains D, J, 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, I, D, J
- SO4 · Sulfate ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 10 copies · chains A, B, C, D, E, F, J
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 | 706 | 0.78 | 0.83 | 53 | empty |
| 2 | 1035 | 0.78 | 0.80 | 80 | MN |
| 3 | 653 | 0.78 | 0.83 | 52 | empty |
| 4 | 697 | 0.74 | 0.80 | 60 | empty |
| 5 | 532 | 0.73 | 0.82 | 59 | empty |
Interfaces
16 interfaces between chains.
- H–L · 1995 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1972 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1853 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1710 Ų buried · 20 hydrogen bonds · protein-protein
- C–H · 657 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 31 disulfide, 4 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 3ZE2 · PDBe 3ZE2 · UniProt P08514 · UniProt P05106
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