MolNFT v1 · #189608 · protein
Structure of the SARS-cov-2 spike glycoprotein in complex with a human single domain antibody N3113 (udd-state, state 1)
7VNC: “Structure of the SARS-cov-2 spike glycoprotein in complex with a human single domain antibody N3113…”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.88). MolNFT v1 #189608 on GenesisL1: 3D structure, binding…
- PDB
- 7VNC
- Type
- protein
- Length
- 3,325 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; N3113
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 3 distinct chains · 20% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A | Spike glycoprotein | protein | 1070 | 21% helix, 27% strand | P0DTC2 |
| V | N3113 | protein | 116 | 8% helix, 24% strand | — |
| B | Spike glycoprotein | protein | 1069 | 20% helix, 24% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 51 copies · chains C, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1196 | 0.88 | 0.89 | 139 | empty |
| 2 | 887 | 0.86 | 0.88 | 110 | empty |
| 3 | 1030 | 0.83 | 0.84 | 123 | empty |
| 4 | 927 | 0.83 | 0.85 | 85 | empty |
| 5 | 683 | 0.76 | 0.82 | 86 | empty |
Interfaces
4 interfaces between chains.
- A–B · 5259 Ų buried · 36 hydrogen bonds · protein-protein
- C–B · 4850 Ų buried · 45 hydrogen bonds · protein-protein
- C–A · 4499 Ų buried · 35 hydrogen bonds · protein-protein
- C–V · 821 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 33 glycan, 27 disulfide (N-glycosylation, disulfide).
Compared structures
- 7VNC · Structure of the SARS-CoV-2 spike glycoprotein in complex with a human single domain… · the same entry in another collection · chain C against C, 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 7VNC · PDBe 7VNC · UniProt P0DTC2
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