Research workbench
Spike protein from SARS-COV2 with Fab fragment of enhancing antibody 2490
Analyse Spike protein from SARS-COV2 with Fab fragment of enhancing antibody 2490 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DZY
- Type
- protein
- Length
- 4,677 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Fab heavy chain of enhancing antibody 2490; Fab light chain of…
- UniProt
- P0DTC2
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 3 distinct chains · 19% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1121 | 23% helix, 30% strand | P0DTC2 |
| H, M, O | Fab heavy chain of enhancing antibody 2490 | protein | 225 | 10% helix, 48% strand | — |
| L, N, P | Fab light chain of enhancing antibody 2490 | protein | 213 | 6% helix, 50% strand | — |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1049 | 0.78 | 0.80 | 139 | empty |
| 2 | 792 | 0.76 | 0.81 | 102 | empty |
| 3 | 901 | 0.75 | 0.79 | 97 | empty |
| 4 | 943 | 0.75 | 0.79 | 97 | empty |
| 5 | 626 | 0.75 | 0.82 | 66 | empty |
Interfaces
12 interfaces between chains.
- B–C · 1151 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 950 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 911 Ų buried · 11 hydrogen bonds · protein-protein
- O–P · 405 Ų buried · 7 hydrogen bonds · protein-protein
- M–N · 404 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7DZY · Spike protein from SARS-CoV2 with Fab fragment of enhancing antibody 2490 · the same entry in another collection · chain B against B, 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 P0DTC2
- Elsewhere: RCSB PDB 7DZY · PDBe 7DZY · UniProt P0DTC2
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