MolNFT v1 · #176980 · protein
Crystal structure of SARS-cov-2 receptor binding domain in complex with neutralizing antibody NCOV617
7E3O · NCOV617 light chain: “Crystal structure of SARS-cov-2 receptor binding domain in complex with neutralizing antibody NCOV617”. X-ray diffraction, 7 pockets (best druggability 0.49). MolNFT v1 #176980 on GenesisL1: 3D structure…
- PDB
- 7E3O
- Type
- protein
- Length
- 615 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NCOV617 light chain; NCOV617 heigh chain; Spike protein S1
- UniProt
- P0DTC2
- Pockets
- 7 · best druggability 0.49
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | NCOV617 light chain | protein | 210 | 7% helix, 48% strand | — |
| H | NCOV617 heigh chain | protein | 216 | 8% helix, 51% strand | — |
| R | Spike protein S1 | protein | 189 | 15% helix, 28% strand | P0DTC2 |
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 265 | 0.49 | 0.73 | 44 | empty |
| 2 | 130 | 0.47 | 0.78 | 23 | empty |
| 3 | 165 | 0.47 | 0.77 | 25 | empty |
| 4 | 73 | 0.41 | 0.80 | 19 | empty |
| 5 | 80 | 0.40 | 0.78 | 14 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1711 Ų buried · 10 hydrogen bonds · protein-protein
- H–R · 719 Ų buried · 8 hydrogen bonds · protein-protein
- L–R · 493 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 7E3O · Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing… · the same entry in another collection · chain L against L, 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 7E3O · PDBe 7E3O · UniProt P0DTC2
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