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
- 5E6S
- Type
- protein
- Length
- 3,102 residues
- Chains
- 6
- 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
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 16% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-L | protein | 579 | 14% helix, 38% strand | P20701 |
| B, D, F | Integrin beta-2 | protein | 455 | 25% helix, 28% strand | P05107 |
| C | Integrin alpha-L | protein | 578 | 14% helix, 38% strand | P20701 |
| E | Integrin alpha-L | protein | 580 | 13% helix, 37% strand | P20701 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B, C, D, E, F
- CA · Calcium ion · metal · 15 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 3 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 791 | 0.85 | 0.87 | 75 | empty |
| 2 | 817 | 0.84 | 0.86 | 74 | empty |
| 3 | 802 | 0.84 | 0.86 | 73 | empty |
| 4 | 859 | 0.72 | 0.77 | 92 | empty |
| 5 | 667 | 0.68 | 0.77 | 73 | empty |
Interfaces
7 interfaces between chains.
- E–F · 1808 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1775 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1755 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 855 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 769 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 5E6S · Structures of leukocyte integrin aLB2: The aI domain, the headpiece, and the pocket for… · the same entry in another collection · chain F against F, TM-score 1.00
- P20701 · AlphaFold monomer V2.0 prediction for integrin alpha-L (P20701) · a predicted model of the same protein · chain C against A, TM-score 1.00
- P05107 · AlphaFold monomer V2.0 prediction for integrin beta-2 (P05107) · a predicted model of the same protein · chain B against A, TM-score 0.92
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 5E6S · PDBe 5E6S · UniProt P20701 · UniProt P05107
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