MolNFT v1 · #180840 · protein
Structure of SARS-cov-2 S protein in complex with N-terminal domain antibody DH1050.1
7LCN · Spike glycoprotein: “Structure of SARS-cov-2 S protein in complex with N-terminal domain antibody DH1050.1”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.87). MolNFT v1 #180840 on GenesisL1: 3D structure…
- PDB
- 7LCN
- Type
- protein
- Length
- 4,296 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; DH1050.1 heavy chain; DH1050.1 light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 18% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A, K | Spike glycoprotein | protein | 993 | 24% helix, 32% strand | P0DTC2 |
| H, B, M | DH1050.1 heavy chain | protein | 223 | 3% helix, 36% strand | — |
| L, D, S | DH1050.1 light chain | protein | 216 | 6% helix, 37% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 63 copies · chains C, A, K
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 | 807 | 0.87 | 0.90 | 111 | empty |
| 2 | 1012 | 0.84 | 0.85 | 106 | empty |
| 3 | 958 | 0.82 | 0.84 | 110 | empty |
| 4 | 671 | 0.79 | 0.84 | 71 | empty |
| 5 | 530 | 0.79 | 0.86 | 80 | empty |
Interfaces
9 interfaces between chains.
- C–A · 5040 Ų buried · 40 hydrogen bonds · protein-protein
- A–K · 5005 Ų buried · 49 hydrogen bonds · protein-protein
- C–K · 4972 Ų buried · 43 hydrogen bonds · protein-protein
- M–S · 2274 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 2184 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide, 48 glycan (disulfide, N-glycosylation).
Compared structures
- 7LCN · Structure of SARS-CoV-2 S protein in complex with N-terminal domain antibody DH1050.1 · 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 7LCN · PDBe 7LCN · UniProt P0DTC2
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