MolNFT v1 · #141270 · protein
Cryo-EM structure of polycystic kidney disease-like channel PKD2L1
5Z1W · Polycystic kidney disease 2-like 1 protein: “Cryo-EM structure of polycystic kidney disease-like channel PKD2L1”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.80). MolNFT v1 #141270 on GenesisL1: 3D…
- PDB
- 5Z1W
- Type
- protein
- Length
- 1,716 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polycystic kidney disease 2-like 1 protein
- UniProt
- A2A259
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 1 distinct chain · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Polycystic kidney disease 2-like 1 protein | protein | 429 | 48% helix, 14% strand | A2A259 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 668 | 0.80 | 0.85 | 80 | empty |
| 2 | 630 | 0.79 | 0.85 | 71 | empty |
| 3 | 638 | 0.79 | 0.84 | 70 | empty |
| 4 | 654 | 0.78 | 0.83 | 71 | empty |
| 5 | 422 | 0.75 | 0.83 | 47 | empty |
Interfaces
4 interfaces between chains.
- A–D · 2836 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 2831 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 2830 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 2819 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 5Z1W · Cryo-EM structure of polycystic kidney disease-like channel PKD2L1 · the same entry in another collection · chain A against A, TM-score 1.00
- A2A259 · AlphaFold monomer V2.0 prediction for polycystic kidney disease 2-like 1 protein (A2A259) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 A2A259
- Elsewhere: RCSB PDB 5Z1W · PDBe 5Z1W · UniProt A2A259
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