Research workbench
Integrin ALPHAIIBBETA3 in complex with ro-435054
Analyse Integrin ALPHAIIBBETA3 in complex with ro-435054 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HDB
- 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
- 5YB, NAG, MAN, BMA, CA, MG, SO4, CL
- Pockets
- 20 · best druggability 0.79
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, 42% strand | P08514 |
| B | Integrin beta-3 | protein | 466 | 23% helix, 30% strand | P05106 |
| C | Integrin alpha-iib | protein | 453 | 5% helix, 42% strand | P08514 |
| D | Integrin beta-3 | protein | 471 | 24% helix, 28% strand | P05106 |
| E | Monoclonal antibody 10E5 heavy chain | protein | 214 | 3% helix, 50% strand | — |
| F, L | Monoclonal antibody 10E5 light chain | protein | 214 | 5% helix, 49% strand | — |
| H | Monoclonal antibody 10E5 heavy chain | protein | 216 | 3% helix, 52% strand | — |
Ligands and binding sites
- 5YB · N-(4-carbamimidoylbenzoyl)-beta-alanyl-L-alpha-aspartyl-L-phenylalanine · 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 · 11 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains B, D
- SO4 · Sulfate ion · ion · 6 copies · chains A, C, D, L
- CL · Chloride ion · ion · 2 copies · chains C
- GOL · Glycerol · additive · chains A
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 | 678 | 0.79 | 0.84 | 52 | empty |
| 2 | 664 | 0.78 | 0.83 | 54 | empty |
| 3 | 730 | 0.76 | 0.81 | 56 | SO4 |
| 4 | 977 | 0.76 | 0.78 | 71 | 5YB |
| 5 | 754 | 0.75 | 0.80 | 66 | empty |
Interfaces
11 interfaces between chains.
- E–F · 2064 Ų buried · 15 hydrogen bonds · protein-protein
- H–L · 2042 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1870 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1824 Ų buried · 23 hydrogen bonds · protein-protein
- C–E · 651 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 37 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 5HDB · Integrin alphaIIbbeta3 in complex with Ro-435054 · the same entry in another collection · 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 5HDB · PDBe 5HDB · UniProt P08514 · UniProt P05106
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