Research workbench
SARS-cov 2 spike protein bound to ly-COV555
Analyse SARS-cov 2 spike protein bound to ly-COV555 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L3N
- Type
- protein
- Length
- 3,056 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Ly-COV555 Fab heavy chain; Ly-COV555 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 5 distinct chains · 22% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 820 | 24% helix, 32% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1001 | 23% helix, 32% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1005 | 23% helix, 32% strand | P0DTC2 |
| D | Ly-COV555 Fab heavy chain | protein | 124 | 10% helix, 48% strand | — |
| E | Ly-COV555 Fab light chain | protein | 106 | 3% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 22 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 785 | 0.83 | 0.86 | 104 | empty |
| 2 | 438 | 0.82 | 0.90 | 65 | empty |
| 3 | 1045 | 0.82 | 0.83 | 89 | empty |
| 4 | 469 | 0.82 | 0.89 | 54 | empty |
| 5 | 555 | 0.80 | 0.86 | 67 | empty |
Interfaces
7 interfaces between chains.
- B–C · 5453 Ų buried · 49 hydrogen bonds · protein-protein
- A–C · 4733 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 4341 Ų buried · 39 hydrogen bonds · protein-protein
- D–E · 1004 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 785 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 37 disulfide, 19 glycan (disulfide, N-glycosylation).
Compared structures
- 7L3N · SARS-CoV 2 Spike Protein bound to LY-CoV555 · 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
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 7L3N · PDBe 7L3N · UniProt P0DTC2
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