Research workbench
Crystal structure of the third PDZ domain from the synaptic protein psd-95 with incorporated azidohomoalanine
Analyse Crystal structure of the third PDZ domain from the synaptic protein psd-95 with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MZ7
- Type
- protein
- Length
- 393 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Disks large homolog 4
- UniProt
- P31016
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Disks large homolog 4 | protein | 100 | 19% helix, 33% strand | P31016 |
| C | Disks large homolog 4 | protein | 97 | 24% helix, 36% strand | P31016 |
| D | Disks large homolog 4 | protein | 96 | 22% helix, 36% strand | P31016 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 631 | 0.66 | 0.76 | 64 | empty |
| 2 | 112 | 0.47 | 0.79 | 28 | empty |
| 3 | 113 | 0.39 | 0.75 | 21 | empty |
| 4 | 71 | 0.35 | 0.76 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–B · 544 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 333 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 317 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 270 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 226 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 5MZ7 · Crystal Structure of the third PDZ domain from the synaptic protein PSD-95 with… · the same entry in another collection · chain D against D, TM-score 1.00
- P31016 · AlphaFold monomer V2.0 prediction for disks large homolog 4 (P31016) · 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 P31016
- Elsewhere: RCSB PDB 5MZ7 · PDBe 5MZ7 · UniProt P31016
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.