MolNFT v1 · #135710 · protein
Crystal structure of human niemann-pick C1 protein
5U73: “Crystal structure of human niemann-pick C1 protein”. X-ray diffraction, 2 ligands (NAG, MAN), 8 pockets (best druggability 0.88). MolNFT v1 #135710 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5U73
- Type
- protein
- Length
- 898 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Niemann-pick C1 protein
- UniProt
- O15118
- Ligands
- NAG, MAN
- Pockets
- 8 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Niemann-pick C1 protein | protein | 898 | 55% helix, 6% strand | O15118 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1091 | 0.88 | 0.88 | 93 | empty |
| 2 | 204 | 0.56 | 0.79 | 19 | empty |
| 3 | 234 | 0.56 | 0.78 | 40 | empty |
| 4 | 59 | 0.38 | 0.80 | 13 | empty |
| 5 | 63 | 0.37 | 0.78 | 13 | empty |
Modifications
Observed in the structure: 12 glycan, 6 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 5U73 · Crystal structure of human Niemann-Pick C1 protein · the same entry in another collection · chain A against A, TM-score 1.00
- O15118 · AlphaFold monomer V2.0 prediction for npc intracellular cholesterol transporter 1 (O15118) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 O15118
- Elsewhere: RCSB PDB 5U73 · PDBe 5U73 · UniProt O15118
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