Research workbench
Crystal structure of an extended B3 integrin L33
Analyse Crystal structure of an extended B3 integrin L33 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BXF
- Type
- protein
- Length
- 927 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chimera protein of integrin beta-3 and integrin alpha-L
- UniProt
- P05106, P20701
- Ligands
- NAG, CA, MG
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chimera protein of integrin beta-3 and integrin alpha-L | protein | 463 | 19% helix, 27% strand | P05106, P20701 |
| B | Chimera protein of integrin beta-3 and integrin alpha-L | protein | 464 | 16% helix, 27% strand | P05106, P20701 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B
- CA · Calcium ion · metal · chains A
- MG · Magnesium ion · metal · chains B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 287 | 0.65 | 0.82 | 39 | empty |
| 2 | 303 | 0.63 | 0.80 | 45 | empty |
| 3 | 364 | 0.55 | 0.74 | 38 | empty |
| 4 | 337 | 0.54 | 0.74 | 39 | empty |
Modifications
Observed in the structure: 26 disulfide, 7 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 P05106
- Every structure of UniProt P20701
- Elsewhere: RCSB PDB 6BXF · PDBe 6BXF · UniProt P05106 · UniProt P20701
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