Research workbench
SARS-cov-2 M protein dimer (long form) in complex with YN7756_1 Fab
Analyse SARS-cov-2 M protein dimer (long form) in complex with YN7756_1 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VGR
- Type
- protein
- Length
- 1,272 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- YN7756_1 Fab light chain; YN7756_1 Fab heavy chain; Membrane protein
- UniProt
- P0DTC5
- Pockets
- 17 · best druggability 0.79
Structure
electron microscopy · 3 distinct chains · 17% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, E | YN7756_1 Fab light chain | protein | 218 | 6% helix, 51% strand | — |
| D, F | YN7756_1 Fab heavy chain | protein | 220 | 4% helix, 47% strand | — |
| A, B | Membrane protein | protein | 198 | 43% helix, 20% strand | P0DTC5 |
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 450 | 0.79 | 0.87 | 48 | empty |
| 2 | 463 | 0.59 | 0.74 | 60 | empty |
| 3 | 94 | 0.57 | 0.86 | 24 | empty |
| 4 | 99 | 0.56 | 0.85 | 20 | empty |
| 5 | 374 | 0.56 | 0.74 | 57 | empty |
Interfaces
11 interfaces between chains.
- A–B · 3074 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 1865 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1860 Ų buried · 17 hydrogen bonds · protein-protein
- D–A · 549 Ų buried · 5 hydrogen bonds · protein-protein
- F–B · 544 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7VGR · SARS-CoV-2 M protein dimer (long form) in complex with YN7756_1 Fab · the same entry in another collection · chain C against C, TM-score 1.00
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 P0DTC5
- Elsewhere: RCSB PDB 7VGR · PDBe 7VGR · UniProt P0DTC5
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