Research workbench
Crystal structure of SARS-cov-2 rbd in complex with antibody nt-193
Analyse Crystal structure of SARS-cov-2 rbd in complex with antibody nt-193 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E5O
- Type
- protein
- Length
- 621 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nt-193 heavy chain; Nt-193 light chain; Spike protein S1
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Nt-193 heavy chain | protein | 220 | 4% helix, 50% strand | — |
| L | Nt-193 light chain | protein | 213 | 6% helix, 50% strand | — |
| A | Spike protein S1 | protein | 188 | 14% helix, 24% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.75 | 0.99 | 17 | empty |
| 2 | 227 | 0.54 | 0.77 | 29 | empty |
| 3 | 225 | 0.48 | 0.74 | 35 | empty |
| 4 | 65 | 0.42 | 0.81 | 14 | empty |
| 5 | 81 | 0.38 | 0.77 | 15 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1913 Ų buried · 13 hydrogen bonds · protein-protein
- L–A · 650 Ų buried · 10 hydrogen bonds · protein-protein
- H–A · 560 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7E5O · Crystal structure of SARS-CoV-2 RBD in complex with antibody NT-193 · the same entry in another collection · chain H against H, 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 7E5O · PDBe 7E5O · UniProt P0DTC2
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