Research workbench
Crystal structure of psd-95 gk domain in complex with phospho-sapap peptide
Analyse Crystal structure of psd-95 gk domain in complex with phospho-sapap peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YPO
- Type
- protein
- Length
- 392 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Disks large homolog 4; Sapap
- UniProt
- P31016
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Disks large homolog 4 | protein | 183 | 44% helix, 20% strand | P31016 |
| A | Disks large homolog 4 | protein | 181 | 45% helix, 20% strand | P31016 |
| C, D | Sapap | protein | 14 | 50% helix, 0% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 726 | 0.71 | 0.77 | 66 | GOL |
| 2 | 315 | 0.58 | 0.77 | 35 | empty |
Interfaces
4 interfaces between chains.
- A–D · 665 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 590 Ų buried · 9 hydrogen bonds · protein-protein
- B–A · 544 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 205 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 5YPO · Crystal structure of PSD-95 GK domain in complex with phospho-SAPAP peptide · the same entry in another collection · chain B against B, TM-score 1.00
- P31016 · AlphaFold monomer V2.0 prediction for disks large homolog 4 (P31016) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 5YPO · PDBe 5YPO · UniProt P31016
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