MolNFT v1 · #180759 · protein
Structure of SARS-cov-2 S protein in complex with N-terminal domain antibody DH1052
7LAB · DH1052 light chain: “Structure of SARS-cov-2 S protein in complex with N-terminal domain antibody DH1052”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.85). MolNFT v1 #180759 on GenesisL1: 3D structure…
- PDB
- 7LAB
- Type
- protein
- Length
- 4,194 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DH1052 light chain; DH1052 heavy chain; Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 18% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X, S, L | DH1052 light chain | protein | 199 | 7% helix, 46% strand | — |
| Y, T, H | DH1052 heavy chain | protein | 227 | 5% helix, 47% strand | — |
| A, B, C | Spike glycoprotein | protein | 972 | 23% helix, 34% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 59 copies · chains A, B, C, H
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 | 878 | 0.85 | 0.87 | 107 | empty |
| 2 | 939 | 0.82 | 0.84 | 99 | empty |
| 3 | 927 | 0.82 | 0.84 | 101 | empty |
| 4 | 507 | 0.82 | 0.88 | 60 | empty |
| 5 | 603 | 0.80 | 0.85 | 58 | empty |
Interfaces
12 interfaces between chains.
- B–C · 5111 Ų buried · 47 hydrogen bonds · protein-protein
- A–C · 5106 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 5014 Ų buried · 48 hydrogen bonds · protein-protein
- S–T · 1935 Ų buried · 15 hydrogen bonds · protein-protein
- H–L · 1920 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide, 43 glycan (disulfide, N-glycosylation).
Compared structures
- 7LAB · Structure of SARS-CoV-2 S protein in complex with N-terminal domain antibody DH1052 · the same entry in another collection · chain X against X, 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 7LAB · PDBe 7LAB · UniProt P0DTC2
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