MolNFT v1 · #189610 · protein
Structure of the SARS-cov-2 spike glycoprotein in complex with a human single domain antibody N3113.1 (uuu-state)
7VNE: “Structure of the SARS-cov-2 spike glycoprotein in complex with a human single domain antibody N3113.1…”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.83). MolNFT v1 #189610 on GenesisL1: 3D structure, binding…
- PDB
- 7VNE
- Type
- protein
- Length
- 3,558 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; N3113.1
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 18% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A, B | Spike glycoprotein | protein | 1070 | 19% helix, 26% strand | P0DTC2 |
| W, U, V | N3113.1 | protein | 116 | 6% helix, 9% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 67 copies · chains C, B, A
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 | 1171 | 0.83 | 0.85 | 126 | empty |
| 2 | 1140 | 0.83 | 0.84 | 116 | empty |
| 3 | 763 | 0.82 | 0.85 | 67 | empty |
| 4 | 982 | 0.79 | 0.81 | 81 | empty |
| 5 | 947 | 0.79 | 0.81 | 70 | empty |
Interfaces
7 interfaces between chains.
- A–B · 4414 Ų buried · 38 hydrogen bonds · protein-protein
- C–B · 4376 Ų buried · 32 hydrogen bonds · protein-protein
- C–A · 4370 Ų buried · 41 hydrogen bonds · protein-protein
- C–W · 912 Ų buried · 6 hydrogen bonds · protein-protein
- A–U · 665 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 glycan, 24 disulfide (N-glycosylation, disulfide, glycation).
Compared structures
- 7VNE · 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 7VNE · PDBe 7VNE · UniProt P0DTC2
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