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Crystallographic structure of neutralizing antibody 2-51 in complex with SARS-cov-2 spike N-terminal domain (ntd)
Analyse Crystallographic structure of neutralizing antibody 2-51 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L2C
- Type
- protein
- Length
- 1,428 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; 2-51 heavy chain; 2-51 light chain
- UniProt
- P0DTC2
- Ligands
- NAG, CA
- Pockets
- 16 · best druggability 0.69
Structure
x-ray diffraction · 5 distinct chains · 5% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 286 | 3% helix, 52% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 273 | 3% helix, 54% strand | P0DTC2 |
| H | 2-51 heavy chain | protein | 221 | 7% helix, 52% strand | — |
| L, D | 2-51 light chain | protein | 213 | 8% helix, 49% strand | — |
| C | 2-51 heavy chain | protein | 222 | 7% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains B, A, H
- CA · Calcium ion · metal · 39 copies · chains A, B, H, L, C, D
- ACT · Acetate ion · additive · 9 copies · chains A, H, B, C, L, D
- CAC · Cacodylate ion · additive · chains A
- PGE · Triethylene glycol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 773 | 0.69 | 0.76 | 63 | CA |
| 2 | 308 | 0.62 | 0.79 | 31 | empty |
| 3 | 422 | 0.57 | 0.74 | 59 | CA |
| 4 | 254 | 0.54 | 0.76 | 30 | CA |
| 5 | 85 | 0.49 | 0.83 | 24 | CA |
Interfaces
7 interfaces between chains.
- C–D · 1870 Ų buried · 12 hydrogen bonds · protein-protein
- H–L · 1666 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 819 Ų buried · 17 hydrogen bonds · protein-protein
- A–H · 816 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 568 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 14 glycan (disulfide, N-glycosylation).
Compared structures
- 7L2C · Crystallographic structure of neutralizing antibody 2-51 in complex with SARS-CoV-2 spike… · 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 7L2C · PDBe 7L2C · UniProt P0DTC2
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