MolNFT v1 · #183421 · protein
Crystal structure of the SARS-cov-2 receptor binding domain in complex with antibody ion-360
7NP1 · Spike protein S1: “Crystal structure of the SARS-cov-2 receptor binding domain in complex with antibody ion-360”. X-ray diffraction, 2 ligands (NAG, FUC), 20 pockets (best druggability 0.83). MolNFT v1 #183421 on GenesisL1: 3D…
- PDB
- 7NP1
- Type
- protein
- Length
- 2,437 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; Immunoglobulin gamma-1 heavy chain; Immunoblobulin light chain
- UniProt
- P0DTC2
- Ligands
- NAG, FUC
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 9 distinct chains · 10% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 171 | 17% helix, 29% strand | P0DTC2 |
| B | Spike protein S1 | protein | 168 | 13% helix, 28% strand | P0DTC2 |
| C | Spike protein S1 | protein | 190 | 18% helix, 29% strand | P0DTC2 |
| D | Spike protein S1 | protein | 181 | 16% helix, 28% strand | P0DTC2 |
| H | Immunoglobulin gamma-1 heavy chain | protein | 220 | 5% helix, 50% strand | — |
| I | Immunoglobulin gamma-1 heavy chain | protein | 216 | 7% helix, 50% strand | — |
| J | Immunoglobulin gamma-1 heavy chain | protein | 218 | 10% helix, 50% strand | — |
| K | Immunoglobulin gamma-1 heavy chain | protein | 217 | 7% helix, 51% strand | — |
| L, M, N, O | Immunoblobulin light chain | protein | 214 | 5% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, C, B, D
- FUC · alpha-L-fucopyranose · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 831 | 0.83 | 0.86 | 88 | empty |
| 2 | 427 | 0.78 | 0.86 | 57 | empty |
| 3 | 1000 | 0.77 | 0.79 | 111 | empty |
| 4 | 362 | 0.69 | 0.82 | 46 | empty |
| 5 | 307 | 0.59 | 0.77 | 48 | empty |
Interfaces
20 interfaces between chains.
- H–L · 1860 Ų buried · 18 hydrogen bonds · protein-protein
- I–M · 1765 Ų buried · 17 hydrogen bonds · protein-protein
- J–N · 1716 Ų buried · 18 hydrogen bonds · protein-protein
- K–O · 1697 Ų buried · 19 hydrogen bonds · protein-protein
- A–H · 783 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 7NP1 · Crystal Structure of the SARS-CoV-2 Receptor Binding Domain in Complex with Antibody… · 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 7NP1 · PDBe 7NP1 · UniProt P0DTC2
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