MolNFT v1 · #125036 · protein
Structure of human NPC1 middle lumenal domain bound to NPC2
5KWY · Niemann-pick C1 protein: “Structure of human NPC1 middle lumenal domain bound to NPC2”. X-ray diffraction, 2 ligands (C3S, NAG), 9 pockets (best druggability 0.77). MolNFT v1 #125036 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5KWY
- Type
- protein
- Length
- 709 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Niemann-pick C1 protein; Epididymal secretory protein E1
- UniProt
- O15118, P61916
- Ligands
- C3S, NAG
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Niemann-pick C1 protein | protein | 208 | 31% helix, 25% strand | O15118 |
| B | Niemann-pick C1 protein | protein | 236 | 37% helix, 20% strand | O15118 |
| C | Epididymal secretory protein E1 | protein | 133 | 2% helix, 56% strand | P61916 |
| D | Epididymal secretory protein E1 | protein | 132 | 2% helix, 56% strand | P61916 |
Ligands and binding sites
- C3S · Cholest-5-en-3-yl hydrogen sulfate · ligand · 2 copies · chains C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 276 | 0.77 | 0.88 | 29 | C3S |
| 2 | 258 | 0.76 | 0.88 | 28 | C3S |
| 3 | 247 | 0.52 | 0.76 | 38 | empty |
| 4 | 271 | 0.49 | 0.73 | 40 | empty |
| 5 | 168 | 0.41 | 0.73 | 25 | empty |
Interfaces
5 interfaces between chains.
- A–B · 808 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 587 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 509 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 153 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 133 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5KWY · Structure of human NPC1 middle lumenal domain bound to NPC2 · the same entry in another collection · chain D against D, TM-score 1.00
- P61916 · AlphaFold monomer V2.0 prediction for npc intracellular cholesterol transporter 2 (P61916) · a predicted model of the same protein · chain D against A, TM-score 0.98
- 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 0.98
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
- Every structure of UniProt P61916
- Elsewhere: RCSB PDB 5KWY · PDBe 5KWY · UniProt O15118 · UniProt P61916
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