Research workbench
Crystal structure of VP12E7 Fab in complex with SARS-cov-2 S fusion peptide
Analyse Crystal structure of VP12E7 Fab in complex with SARS-cov-2 S fusion peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SL5
- Type
- protein
- Length
- 1,823 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain VP12E7 Fab; Light chain VP12E7 Fab…
- Pockets
- 18 · best druggability 0.77
Structure
x-ray diffraction · 9 distinct chains · 11% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heavy chain VP12E7 Fab | protein | 228 | 9% helix, 49% strand | — |
| B, K | Light chain VP12E7 Fab | protein | 214 | 7% helix, 50% strand | — |
| C, F | Pro-ser-lys-arg-ser-phe-ile-glu-asp-leu-leu-phe-asn | protein | 14 | 71% helix, 0% strand | — |
| D | Heavy chain VP12E7 Fab | protein | 228 | 10% helix, 49% strand | — |
| E, H | Light chain VP12E7 Fab | protein | 215 | 7% helix, 49% strand | — |
| G | Heavy chain VP12E7 Fab | protein | 229 | 11% helix, 48% strand | — |
| I | Pro-ser-lys-arg-ser-phe-ile-glu-asp-leu-leu-phe-asn | protein | 13 | 77% helix, 0% strand | — |
| J | Heavy chain VP12E7 Fab | protein | 227 | 7% helix, 50% strand | — |
| L | Pro-ser-lys-arg-ser-phe-ile-glu-asp-leu-leu-phe-asn | protein | 12 | 83% helix, 0% strand | — |
Pockets
18 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 663 | 0.77 | 0.82 | 88 | empty |
| 2 | 494 | 0.65 | 0.77 | 63 | empty |
| 3 | 322 | 0.55 | 0.75 | 41 | empty |
| 4 | 340 | 0.55 | 0.74 | 43 | empty |
| 5 | 157 | 0.54 | 0.81 | 30 | empty |
Interfaces
16 interfaces between chains.
- A–B · 2023 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 2022 Ų buried · 20 hydrogen bonds · protein-protein
- G–H · 2019 Ų buried · 19 hydrogen bonds · protein-protein
- J–K · 1996 Ų buried · 18 hydrogen bonds · protein-protein
- B–K · 942 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 7SL5 · Crystal Structure of VP12E7 Fab in complex with SARS-CoV-2 S fusion peptide · the same entry in another collection · chain A against A, 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
- Elsewhere: RCSB PDB 7SL5 · PDBe 7SL5
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