Research workbench
NPC1-NPC2 complex structure at pH 5.5
Analyse NPC1-NPC2 complex structure at pH 5.5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6W5V
- Type
- protein
- Length
- 1,307 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Npc intracellular cholesterol transporter 1; Npc intracellular cholesterol transporter 2
- UniProt
- O15118, P61916
- Ligands
- CLR, NAG, BMA
- Pockets
- 18 · best druggability 0.89
Structure
electron microscopy · 2 distinct chains · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Npc intracellular cholesterol transporter 1 | protein | 1175 | 52% helix, 8% strand | O15118 |
| D | Npc intracellular cholesterol transporter 2 | protein | 132 | 3% helix, 53% strand | P61916 |
Ligands and binding sites
- CLR · Cholesterol · ligand · 3 copies · chains A, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains A, D
- BMA · beta-D-mannopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 966 | 0.89 | 0.90 | 109 | CLR |
| 2 | 1047 | 0.80 | 0.81 | 84 | CLR |
| 3 | 435 | 0.78 | 0.86 | 43 | CLR |
| 4 | 83 | 0.76 | 0.97 | 24 | empty |
| 5 | 405 | 0.65 | 0.78 | 36 | empty |
Interfaces
1 interface between chains.
- A–D · 530 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 14 glycan (disulfide, N-glycosylation).
Compared structures
- 6W5V · NPC1-NPC2 complex structure at pH 5.5 · the same entry in another collection · chain A against A, 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 0.96
- 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 0.90
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 6W5V · PDBe 6W5V · UniProt O15118 · UniProt P61916
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