Research workbench
Crystal structure of icam-5 in complex with al I domain
Analyse Crystal structure of icam-5 in complex with al I domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BN3
- Type
- protein
- Length
- 376 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-L; Intercellular adhesion molecule 5
- UniProt
- P20701, Q9UMF0
- Ligands
- NAG, MG
- Pockets
- 5 · best druggability 0.44
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-L | protein | 180 | 43% helix, 22% strand | P20701 |
| B | Intercellular adhesion molecule 5 | protein | 196 | 5% helix, 58% strand | Q9UMF0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains B
- MG · Magnesium ion · metal · chains A, B
- GOL · Glycerol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.44 | 0.78 | 19 | empty |
| 2 | 114 | 0.42 | 0.77 | 14 | empty |
| 3 | 59 | 0.37 | 0.79 | 13 | empty |
| 4 | 53 | 0.33 | 0.78 | 14 | empty |
| 5 | 61 | 0.29 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 814 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 glycan, 3 disulfide (N-glycosylation, disulfide).
Compared structures
- 3BN3 · crystal structure of ICAM-5 in complex with aL I domain · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UMF0 · AlphaFold monomer V2.0 prediction for intercellular adhesion molecule 5 (Q9UMF0) · a predicted model of the same protein · chain B against A, TM-score 0.95
- P20701 · AlphaFold monomer V2.0 prediction for integrin alpha-L (P20701) · a predicted model of the same protein · chain A against A, TM-score 0.87
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 Q9UMF0
- Elsewhere: RCSB PDB 3BN3 · PDBe 3BN3 · UniProt P20701 · UniProt Q9UMF0
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