MolNFT v1 · #102322 · protein
Crystal structure of icam-5 D1-D4 ectodomain fragment, space group P4322
4OIA · Intercellular adhesion molecule 5: “Crystal structure of icam-5 D1-D4 ectodomain fragment, space group P4322”. X-ray diffraction, 2 ligands (NAG, BMA), 1 pocket (best druggability 0.48). MolNFT v1 #102322 on GenesisL1: 3D structure…
- PDB
- 4OIA
- Type
- protein
- Length
- 749 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Intercellular adhesion molecule 5
- UniProt
- Q9UMF0
- Ligands
- NAG, BMA
- Pockets
- 1 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Intercellular adhesion molecule 5 | protein | 374 | 2% helix, 52% strand | Q9UMF0 |
| B | Intercellular adhesion molecule 5 | protein | 375 | 3% helix, 55% strand | Q9UMF0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 26 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 3 copies
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.48 | 0.80 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 182 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 glycan, 10 disulfide (N-glycosylation, disulfide).
Compared structures
- 4OIA · Crystal Structure of ICAM-5 D1-D4 ectodomain fragment, Space Group P4322 · 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 0.92
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 Q9UMF0
- Elsewhere: RCSB PDB 4OIA · PDBe 4OIA · UniProt Q9UMF0
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