Research workbench
Crystal structure of the 3RD PDZ domain of intestine- and kidney- enriched PDZ domain ikepp (PDZD3)
Analyse Crystal structure of the 3RD PDZ domain of intestine- and kidney- enriched PDZ… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2V90
- Type
- protein
- Length
- 566 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PDZ domain-containing protein 3
- UniProt
- Q86UT5
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, F | PDZ domain-containing protein 3 | protein | 95 | 14% helix, 40% strand | Q86UT5 |
| C, D | PDZ domain-containing protein 3 | protein | 93 | 14% helix, 43% strand | Q86UT5 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 276 | 0.51 | 0.74 | 29 | empty |
| 2 | 240 | 0.49 | 0.74 | 27 | empty |
| 3 | 177 | 0.48 | 0.76 | 35 | empty |
| 4 | 106 | 0.41 | 0.77 | 23 | empty |
| 5 | 90 | 0.38 | 0.76 | 22 | empty |
Interfaces
8 interfaces between chains.
- C–E · 1666 Ų buried · 32 hydrogen bonds · protein-protein
- D–F · 1633 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 450 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 442 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 282 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2V90 · Crystal structure of the 3rd PDZ domain of intestine- and kidney- enriched PDZ domain… · the same entry in another collection · chain F against F, TM-score 1.00
- Q86UT5 · AlphaFold monomer V2.0 prediction for NA(+)/H(+) exchange regulatory cofactor nhe-RF4… · a predicted model of the same protein · chain C against A, TM-score 0.85
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 Q86UT5
- Elsewhere: RCSB PDB 2V90 · PDBe 2V90 · UniProt Q86UT5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.