Research workbench
Cryoem structure of human polycystin-2/PKD2 in udm supplemented with PI(3,5)P2
Analyse Cryoem structure of human polycystin-2/PKD2 in udm supplemented with PI(3,5)P2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6T9O
- Type
- protein
- Length
- 1,924 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 · 54% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Polycystin-2 | protein | 481 | 54% helix, 10% strand | Q13563 |
Ligands and binding sites
- UMQ · Undecyl-maltoside · ligand · 20 copies · chains A, B, C, D
- 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1055 | 0.84 | 0.84 | 129 | UMQ |
| 2 | 1116 | 0.83 | 0.84 | 140 | UMQ |
| 3 | 1088 | 0.83 | 0.84 | 119 | UMQ |
| 4 | 1072 | 0.83 | 0.83 | 118 | UMQ |
| 5 | 147 | 0.82 | 0.98 | 24 | CA |
Interfaces
6 interfaces between chains.
- A–D · 3613 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 3613 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 3607 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 3606 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 49 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 6T9O · CryoEM structure of human polycystin-2/PKD2 in UDM supplemented with PI(3,5)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 0.98
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 Q13563
- Elsewhere: RCSB PDB 6T9O · PDBe 6T9O · UniProt Q13563
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