Research workbench
Crystal structure of the extracellular segment of integrin alpha VBETA3 bound to MN2+
Analyse Crystal structure of the extracellular segment of integrin alpha VBETA3 bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1M1X
- Type
- protein
- Length
- 1,466 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-V; Integrin beta-3
- UniProt
- P05106
- Ligands
- NAG, NDG, MN
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-V | protein | 927 | 2% helix, 41% strand | — |
| B | Integrin beta-3 | protein | 539 | 16% helix, 24% strand | P05106 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A, B
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 3 copies · chains A, B
- MN · Manganese (II) ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 920 | 0.80 | 0.82 | 81 | empty |
| 2 | 683 | 0.77 | 0.82 | 57 | empty |
| 3 | 547 | 0.65 | 0.76 | 46 | NAG |
| 4 | 77 | 0.43 | 0.80 | 19 | empty |
| 5 | 108 | 0.42 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2883 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 25 disulfide, 11 glycan (disulfide, N-glycosylation).
Compared structures
- 1M1X · Crystal structure of the extracellular segment of integrin alpha VBETA3 bound to MN2+ · the same entry in another collection · chain A 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 0.96
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 P05106
- Elsewhere: RCSB PDB 1M1X · PDBe 1M1X · UniProt P05106
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