MolNFT v1 · #17821 · protein
The crystal structure of icam-1 D3-D5 fragment
1P53 · Intercellular adhesion molecule-1: “The crystal structure of icam-1 D3-D5 fragment”. X-ray diffraction, 1 ligand (NAG), 1 pocket (best druggability 0.46). MolNFT v1 #17821 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1P53
- Type
- protein
- Length
- 500 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Intercellular adhesion molecule-1
- UniProt
- P05362
- Ligands
- NAG
- Pockets
- 1 · best druggability 0.46
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 60% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Intercellular adhesion molecule-1 | protein | 250 | 5% helix, 60% strand | P05362 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
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 | 236 | 0.46 | 0.73 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1151 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
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
- Elsewhere: RCSB PDB 1P53 · PDBe 1P53 · UniProt P05362
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