MolNFT v1 · #164796 · protein
Cryoem structure of human polycystin-2/PKD2 in udm supplemented with PI(4,5)P2
6T9N: “Cryoem structure of human polycystin-2/PKD2 in udm supplemented with PI(4,5)P2”. Electron microscopy, 4 ligands (UMQ, CLR, NAG), 20 pockets (best druggability 0.84). MolNFT v1 #164796 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6T9N
- Type
- protein
- Length
- 1,920 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polycystin-2
- UniProt
- Q13563
- Ligands
- UMQ, CLR, NAG, CA
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 53% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Polycystin-2 | protein | 480 | 53% helix, 11% strand | Q13563 |
Ligands and binding sites
- UMQ · Undecyl-maltoside · ligand · 32 copies · chains A, B, D, C
- CLR · Cholesterol · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B, C, D
- CA · Calcium ion · metal · 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1038 | 0.84 | 0.85 | 115 | UMQ |
| 2 | 993 | 0.84 | 0.85 | 119 | UMQ |
| 3 | 178 | 0.83 | 0.97 | 28 | empty |
| 4 | 1130 | 0.82 | 0.83 | 120 | UMQ |
| 5 | 1164 | 0.82 | 0.83 | 133 | UMQ |
Interfaces
6 interfaces between chains.
- A–D · 3488 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 3482 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 3481 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 3477 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 45 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 6T9N · CryoEM structure of human polycystin-2/PKD2 in UDM supplemented with PI(4,5)P2 · the same entry in another collection · chain A against A, TM-score 1.00
- Q13563 · AlphaFold monomer V2.0 prediction for polycystin-2 (Q13563) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q13563
- Elsewhere: RCSB PDB 6T9N · PDBe 6T9N · UniProt Q13563
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.