Research workbench
Structures of leukocyte integrin ALB2: the ai domain, the headpiece, and the pocket for the internal ligand
Analyse Structures of leukocyte integrin ALB2: the ai domain, the headpiece, and the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E6R
- Type
- protein
- Length
- 1,035 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-L; Integrin beta-2
- UniProt
- P20701, P05107
- Ligands
- NAG, CA, MG
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-L | protein | 581 | 15% helix, 36% strand | P20701 |
| B | Integrin beta-2 | protein | 454 | 24% helix, 30% strand | P05107 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 845 | 0.83 | 0.85 | 71 | empty |
| 2 | 379 | 0.62 | 0.78 | 42 | empty |
| 3 | 57 | 0.61 | 0.92 | 19 | empty |
| 4 | 372 | 0.60 | 0.76 | 36 | empty |
| 5 | 160 | 0.52 | 0.79 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1816 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5E6R · Structures of leukocyte integrin aLb2: The aI domain, the headpiece, and the pocket for… · the same entry in another collection · chain A against A, TM-score 1.00
- P20701 · AlphaFold monomer V2.0 prediction for integrin alpha-L (P20701) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P05107 · AlphaFold monomer V2.0 prediction for integrin beta-2 (P05107) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 P20701
- Every structure of UniProt P05107
- Elsewhere: RCSB PDB 5E6R · PDBe 5E6R · UniProt P20701 · UniProt P05107
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