Research workbench
PALS1 PDZ1 domain with SARS-cov-2_E pbm complex
Analyse PALS1 PDZ1 domain with SARS-cov-2_E pbm complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NTK
- Type
- protein
- Length
- 370 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maguk P55 subfamily member 5; Envelope small membrane protein
- UniProt
- Q8N3R9, P0DTC4
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 18% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, F | Maguk P55 subfamily member 5 | protein | 86 | 20% helix, 42% strand | Q8N3R9 |
| B | Maguk P55 subfamily member 5 | protein | 85 | 20% helix, 41% strand | Q8N3R9 |
| C, E, G | Envelope small membrane protein | protein | 7 | 0% helix, 29% strand | P0DTC4 |
| H | Envelope small membrane protein | protein | 6 | 0% helix, 33% strand | P0DTC4 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, D, E, F
- FLC · Citrate anion · additive · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 532 | 0.64 | 0.76 | 53 | empty |
| 2 | 51 | 0.32 | 0.77 | 11 | EDO |
Interfaces
12 interfaces between chains.
- A–C · 485 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 482 Ų buried · 11 hydrogen bonds · protein-protein
- B–G · 479 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 476 Ų buried · 12 hydrogen bonds · protein-protein
- F–H · 459 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
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 Q8N3R9
- Every structure of UniProt P0DTC4
- Elsewhere: RCSB PDB 7NTK · PDBe 7NTK · UniProt Q8N3R9 · UniProt P0DTC4
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