Research workbench
Crystal structure of the truncated form of the third PDZ domain of psd-95: residues 302-392
Analyse Crystal structure of the truncated form of the third PDZ domain of psd-95… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QJD
- Type
- protein
- Length
- 334 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Disks large homolog 4
- UniProt
- P78352
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Disks large homolog 4 | protein | 83 | 11% helix, 35% strand | P78352 |
| C | Disks large homolog 4 | protein | 85 | 11% helix, 39% strand | P78352 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 684 | 0.80 | 0.84 | 69 | SO4 |
| 2 | 141 | 0.45 | 0.77 | 23 | SO4 |
| 3 | 74 | 0.44 | 0.81 | 21 | empty |
| 4 | 92 | 0.41 | 0.78 | 21 | empty |
| 5 | 92 | 0.39 | 0.77 | 20 | SO4 |
Interfaces
6 interfaces between chains.
- A–B · 557 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 541 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 348 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 258 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 253 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6QJD · Crystal Structure of the truncated form of the third PDZ domain of PSD-95: residues… · the same entry in another collection · chain D against D, TM-score 1.00
- P78352 · AlphaFold monomer V2.0 prediction for disks large homolog 4 (P78352) · a predicted model of the same protein · chain D against A, TM-score 0.95
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 P78352
- Elsewhere: RCSB PDB 6QJD · PDBe 6QJD · UniProt P78352
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