Research workbench
PALS1/MPP5 PDZ domain in complex with SARS-cov-2_E pbm peptide
Analyse PALS1/MPP5 PDZ domain in complex with SARS-cov-2_E pbm peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QCS
- Type
- protein
- Length
- 287 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein PALS1; Envelope small membrane protein
- UniProt
- Q8N3R9, P0DTC4
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein PALS1 | protein | 97 | 14% helix, 36% strand | Q8N3R9 |
| B | Protein PALS1 | protein | 98 | 14% helix, 36% strand | Q8N3R9 |
| C, D | Envelope small membrane protein | protein | 5 | 0% helix, 20% strand | P0DTC4 |
| E | Protein PALS1 | protein | 82 | 11% helix, 43% strand | Q8N3R9 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 140 | 0.55 | 0.81 | 21 | empty |
| 2 | 191 | 0.50 | 0.76 | 31 | empty |
| 3 | 224 | 0.48 | 0.74 | 27 | empty |
Interfaces
6 interfaces between chains.
- A–C · 417 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 407 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 377 Ų buried · 1 hydrogen bond · protein-protein
- A–E · 107 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 42 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7QCS · PALS1/MPP5 PDZ domain in complex with SARS-CoV-2_E PBM peptide · the same entry in another collection · chain E against E, TM-score 1.00
- Q8N3R9 · AlphaFold monomer V2.0 prediction for maguk P55 subfamily member 5 (Q8N3R9) · a predicted model of the same protein · chain E against A, TM-score 0.98
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 7QCS · PDBe 7QCS · UniProt Q8N3R9 · UniProt P0DTC4
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