Research workbench
Integrin alpha IIB beta3 complex with BMS4-3
Analyse Integrin alpha IIB beta3 complex with BMS4-3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UDH
- Type
- protein
- Length
- 2,702 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.99999
- Source
- Homo sapiens; Mus musculus
- Molecule
- Integrin alpha-IIb heavy chain; Isoform Beta-3C of Integrin beta-3; 10E5 Fab heavy chain…
- UniProt
- P08514, P05106
- Ligands
- MWO, NAG, MAN, BMA, CA, MN, SO4, CL
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · resolution 1.99999 · 7 distinct chains · 12% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-IIb heavy chain | protein | 454 | 6% helix, 41% strand | P08514 |
| B | Isoform Beta-3C of Integrin beta-3 | protein | 466 | 24% helix, 30% strand | P05106 |
| C | Integrin alpha-IIb heavy chain | protein | 453 | 7% helix, 41% strand | P08514 |
| D | Isoform Beta-3C of Integrin beta-3 | protein | 471 | 24% helix, 28% strand | P05106 |
| E | 10E5 Fab heavy chain | protein | 214 | 4% helix, 50% strand | — |
| F, L | 10E5 Fab light chain | protein | 214 | 5% helix, 50% strand | — |
| H | 10E5 Fab heavy chain | protein | 216 | 3% helix, 52% strand | — |
Ligands and binding sites
- MWO · (4-{[(5S)-3-(piperidin-4-yl)-4,5-dihydro-1,2-oxazol-5-yl]methyl}piperazin-1-yl)acetic acid · 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 · 4 copies · chains 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, D
- SO4 · Sulfate ion · ion · 9 copies · chains A, C, D, L
- CL · Chloride ion · ion · 3 copies · chains 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 707 | 0.79 | 0.83 | 49 | empty |
| 2 | 676 | 0.78 | 0.83 | 57 | empty |
| 3 | 949 | 0.75 | 0.78 | 69 | MN, MWO |
| 4 | 492 | 0.73 | 0.82 | 50 | empty |
| 5 | 578 | 0.73 | 0.81 | 61 | CL |
Interfaces
11 interfaces between chains.
- E–F · 2056 Ų buried · 18 hydrogen bonds · protein-protein
- H–L · 2038 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1839 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1832 Ų buried · 21 hydrogen bonds · protein-protein
- A–H · 669 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 37 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 7UDH · Integrin ALAPHIIBBETA3 complex with BMS4-3 · 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
- P05106 · AlphaFold monomer V2.0 prediction for integrin beta-3 (P05106) · a predicted model of the same protein · chain B against A, TM-score 0.90
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 7UDH · PDBe 7UDH · UniProt P08514 · UniProt P05106
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