MolNFT v1 · #177136 · protein
Crystal structure of SARS-cov-2 antibody P2C-1F11 with mutated rbd
7E8M · Spike protein S1: “Crystal structure of SARS-cov-2 antibody P2C-1F11 with mutated rbd”. X-ray diffraction, 1 ligand (NAG), 5 pockets (best druggability 0.56). MolNFT v1 #177136 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7E8M
- Type
- protein
- Length
- 615 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; Antibody P2C-1F11 heavy chain; Antibody P2C-1F11 light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Spike protein S1 | protein | 192 | 18% helix, 29% strand | P0DTC2 |
| H | Antibody P2C-1F11 heavy chain | protein | 209 | 9% helix, 52% strand | — |
| L | Antibody P2C-1F11 light chain | protein | 214 | 7% helix, 54% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 203 | 0.56 | 0.80 | 41 | empty |
| 2 | 52 | 0.49 | 0.87 | 22 | empty |
| 3 | 233 | 0.47 | 0.74 | 41 | empty |
| 4 | 127 | 0.40 | 0.74 | 28 | empty |
| 5 | 100 | 0.33 | 0.72 | 18 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1686 Ų buried · 12 hydrogen bonds · protein-protein
- E–H · 738 Ų buried · 17 hydrogen bonds · protein-protein
- E–L · 363 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7E8M · Crystal structure of SARS-CoV-2 antibody P2C-1F11 with mutated RBD · the same entry in another collection · chain E against E, 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 7E8M · PDBe 7E8M · UniProt P0DTC2
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