Research workbench
Crystal structure of alphal I domain in complex with icam-1
Analyse Crystal structure of alphal I domain in complex with icam-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MQ8
- Type
- protein
- Length
- 722 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Intercellular adhesion molecule-1; Integrin alpha-L
- UniProt
- P05362, P20701
- Ligands
- NAG, MG
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Intercellular adhesion molecule-1 | protein | 184 | 2% helix, 47% strand | P05362 |
| B, D | Integrin alpha-L | protein | 177 | 22% helix, 14% strand | P20701 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 539 | 0.71 | 0.80 | 50 | empty |
| 2 | 217 | 0.65 | 0.83 | 32 | empty |
| 3 | 110 | 0.62 | 0.87 | 23 | empty |
| 4 | 276 | 0.55 | 0.77 | 33 | empty |
| 5 | 291 | 0.55 | 0.76 | 38 | empty |
Interfaces
3 interfaces between chains.
- C–D · 659 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 656 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 592 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 1MQ8 · Crystal structure of alphaL I domain in complex with ICAM-1 · the same entry in another collection · chain A against A, TM-score 1.00
- P05362 · AlphaFold monomer V2.0 prediction for intercellular adhesion molecule 1 (P05362) · a predicted model of the same protein · chain A against A, TM-score 0.97
- P20701 · AlphaFold monomer V2.0 prediction for integrin alpha-L (P20701) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 P05362
- Every structure of UniProt P20701
- Elsewhere: RCSB PDB 1MQ8 · PDBe 1MQ8 · UniProt P05362 · UniProt P20701
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