Research workbench
X-ray structure of Lfa-1 I domain in complex with BMS-68852 collected at 273 K
Analyse X-ray structure of Lfa-1 I domain in complex with BMS-68852 collected at 273 K in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KC5
- Type
- protein
- Length
- 364 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.86
- Source
- Homo sapiens
- Molecule
- Integrin alpha-L
- UniProt
- P20701
- Ligands
- BJZ, MG
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · resolution 1.86 · 1 distinct chain · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Integrin alpha-L | protein | 182 | 40% helix, 21% strand | P20701 |
Ligands and binding sites
- BJZ · 6-[(5S,9R)-9-(4-cyanophenyl)-3-(3,5-dichlorophenyl)-1-methyl-2,4-dioxo-1,3,7-triazaspiro[4.4]non-7-yl]pyridine-3-carboxylic acid · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 217 | 0.68 | 0.84 | 24 | BJZ |
| 2 | 210 | 0.65 | 0.83 | 26 | BJZ |
| 3 | 321 | 0.61 | 0.78 | 49 | empty |
Interfaces
1 interface between chains.
- A–C · 382 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7KC5 · X-ray structure of lfa-1 I domain in complex with bms-68852 collected at 273 K · 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 0.97
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 7KC5 · PDBe 7KC5 · UniProt P20701
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