MolNFT v1 · #180521 · protein
Cryo-EM structure of ntd-directed neutralizing antibody 1-87 in complex with prefusion SARS-cov-2 spike glycoprotein
7L2D: “Cryo-EM structure of ntd-directed neutralizing antibody 1-87 in complex with prefusion SARS-cov-2 spike…”. Electron microscopy, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.87). MolNFT v1 #180521 on GenesisL1: 3D structure…
- PDB
- 7L2D
- Type
- protein
- Length
- 3,492 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; 1-87 heavy chain; 1-87 light chain
- UniProt
- P0DTC2
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 4 distinct chains · 19% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1100 | 21% helix, 30% strand | P0DTC2 |
| H | 1-87 heavy chain | protein | 127 | 2% helix, 39% strand | — |
| L | 1-87 light chain | protein | 109 | 3% helix, 38% strand | — |
| B, C | Spike glycoprotein | protein | 1078 | 21% helix, 31% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 74 copies · chains A, C, B
- BMA · beta-D-mannopyranose · sugar · 3 copies
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 | 1125 | 0.87 | 0.88 | 119 | empty |
| 2 | 1171 | 0.85 | 0.86 | 139 | empty |
| 3 | 933 | 0.80 | 0.82 | 99 | empty |
| 4 | 497 | 0.79 | 0.86 | 69 | empty |
| 5 | 1055 | 0.79 | 0.80 | 98 | empty |
Interfaces
6 interfaces between chains.
- A–C · 7148 Ų buried · 73 hydrogen bonds · protein-protein
- A–B · 7020 Ų buried · 66 hydrogen bonds · protein-protein
- B–C · 6825 Ų buried · 61 hydrogen bonds · protein-protein
- A–H · 1091 Ų buried · 20 hydrogen bonds · protein-protein
- H–L · 1023 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 glycan, 44 disulfide (N-glycosylation, disulfide).
Compared structures
- 7L2D · Cryo-EM structure of NTD-directed neutralizing antibody 1-87 in complex with prefusion… · 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 7L2D · PDBe 7L2D · UniProt P0DTC2
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