MolNFT v1 · #66157 · protein
Crystal structure of intermediate affinity I domain of integrin lfa-1 with the Fab fragment of its antibody al-57
3HI6 · Integrin alpha-L: “Crystal structure of intermediate affinity I domain of integrin lfa-1 with the Fab fragment of its antibody…”. X-ray diffraction, 2 ligands (MN, SO4), 15 pockets (best druggability 0.55). MolNFT v1 #66157 on…
- PDB
- 3HI6
- Type
- protein
- Length
- 1,209 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-L; Heavy chain of Fab fragment of al-57 against alpha L I domain; Light…
- UniProt
- P20701
- Ligands
- MN, SO4
- Pockets
- 15 · best druggability 0.55
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Integrin alpha-L | protein | 180 | 37% helix, 21% strand | P20701 |
| H | Heavy chain of Fab fragment of al-57 against alpha L I domain | protein | 213 | 9% helix, 53% strand | — |
| L | Light chain of Fab fragment of al-57 against alpha L I domain | protein | 210 | 6% helix, 51% strand | — |
| X | Heavy chain of Fab fragment of al-57 against alpha L I domain | protein | 217 | 7% helix, 51% strand | — |
| Y | Light chain of Fab fragment of al-57 against alpha L I domain | protein | 209 | 6% helix, 53% strand | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, H, B, X
- SO4 · Sulfate ion · ion · 6 copies · chains B, H, X, L, Y
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 361 | 0.55 | 0.74 | 47 | empty |
| 2 | 88 | 0.52 | 0.84 | 25 | empty |
| 3 | 103 | 0.52 | 0.83 | 25 | empty |
| 4 | 57 | 0.50 | 0.86 | 22 | empty |
| 5 | 92 | 0.41 | 0.78 | 17 | empty |
Interfaces
7 interfaces between chains.
- H–L · 1525 Ų buried · 16 hydrogen bonds · protein-protein
- X–Y · 1520 Ų buried · 16 hydrogen bonds · protein-protein
- H–X · 838 Ų buried · 5 hydrogen bonds · protein-protein
- A–H · 679 Ų buried · 8 hydrogen bonds · protein-protein
- B–X · 678 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 3HI6 · Crystal structure of intermediate affinity I domain of integrin LFA-1 with the Fab… · the same entry in another collection · chain H against H, 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 0.92
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
- Elsewhere: RCSB PDB 3HI6 · PDBe 3HI6 · UniProt P20701
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