Research workbench
Crystal structure of icam-5 D1-D4 ectodomain fragment, space group R3
Analyse Crystal structure of icam-5 D1-D4 ectodomain fragment, space group R3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OIB
- Type
- protein
- Length
- 372 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Intercellular adhesion molecule 5
- UniProt
- Q9UMF0
- Ligands
- NAG, BMA, MAN
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 2% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Intercellular adhesion molecule 5 | protein | 372 | 2% helix, 55% strand | Q9UMF0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 5 copies
- MAN · alpha-D-mannopyranose · sugar · 3 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.70 | 0.95 | 26 | empty |
| 2 | 52 | 0.60 | 0.92 | 22 | empty |
| 3 | 61 | 0.60 | 0.91 | 23 | empty |
| 4 | 71 | 0.58 | 0.88 | 21 | empty |
Modifications
Observed in the structure: 9 glycan, 5 disulfide (N-glycosylation, disulfide).
Compared structures
- 4OIB · Crystal Structure of ICAM-5 D1-D4 ectodomain fragment, Space Group R3 · 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 A against A, TM-score 0.94
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 Q9UMF0
- Elsewhere: RCSB PDB 4OIB · PDBe 4OIB · UniProt Q9UMF0
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