Research workbench
Third PDZ domain (PDZ3) of psd-95 complexed with cfmoc-kketev peptide
Analyse Third PDZ domain (PDZ3) of psd-95 complexed with cfmoc-kketev peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D13
- Type
- protein
- Length
- 425 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Disks large homolog 4; Cfmoc-kketev peptide
- UniProt
- P31016
- Ligands
- 56J, LYS
- Pockets
- 6 · best druggability 0.47
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Disks large homolog 4 | protein | 100 | 26% helix, 35% strand | P31016 |
| C | Disks large homolog 4 | protein | 101 | 25% helix, 33% strand | P31016 |
| G, E, H, F | Cfmoc-kketev peptide | protein | 6 | 0% helix, 33% strand | — |
Ligands and binding sites
- 56J · 3-(9H-fluoren-9-yl)propanal · ligand · 5 copies · chains B, G, A, E, C, H, D, F
- LYS · Lysine · ligand · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.47 | 0.85 | 17 | empty |
| 2 | 86 | 0.39 | 0.77 | 14 | 56J |
| 3 | 77 | 0.35 | 0.75 | 15 | 56J |
| 4 | 67 | 0.32 | 0.75 | 16 | 56J |
| 5 | 62 | 0.32 | 0.75 | 14 | 56J |
Interfaces
7 interfaces between chains.
- B–G · 489 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 423 Ų buried · 11 hydrogen bonds · protein-protein
- C–H · 397 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 383 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 328 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5D13 · Third PDZ domain (PDZ3) of PSD-95 complexed with CFMOC-KKETEV peptide · the same entry in another collection · chain F against F, TM-score 1.00
- P31016 · AlphaFold monomer V2.0 prediction for disks large homolog 4 (P31016) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 5D13 · PDBe 5D13 · UniProt P31016
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