MolNFT v1 · #190226 · protein
Locally refined region of SARS-cov-2 spike in complex with IgG 553-15
7WO7 · MAB15 vh: “Locally refined region of SARS-cov-2 spike in complex with IgG 553-15”. Electron microscopy, 1 ligand (NAG), 5 pockets (best druggability 0.56). MolNFT v1 #190226 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7WO7
- Type
- protein
- Length
- 634 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MAB15 vh; MAB15 vl; Spike protein S1
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.56
Structure
electron microscopy · 3 distinct chains · 4% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MAB15 vh | protein | 225 | 3% helix, 34% strand | — |
| B | MAB15 vl | protein | 215 | 1% helix, 27% strand | — |
| C | Spike protein S1 | protein | 194 | 8% helix, 25% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains C
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 | 187 | 0.56 | 0.80 | 25 | empty |
| 2 | 100 | 0.40 | 0.77 | 19 | empty |
| 3 | 77 | 0.36 | 0.76 | 21 | empty |
| 4 | 104 | 0.33 | 0.73 | 22 | empty |
| 5 | 55 | 0.29 | 0.75 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2000 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 546 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 400 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7WO7 · Locally refined region of SARS-CoV-2 Spike in complex with IgG 553-15 · 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 7WO7 · PDBe 7WO7 · UniProt P0DTC2
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