Research workbench
Cryo-EM structure of ntd-directed neutralizing antibody 5-7 in complex with prefusion SARS-cov-2 spike glycoprotein
Analyse Cryo-EM structure of ntd-directed neutralizing antibody 5-7 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RW2
- Type
- protein
- Length
- 3,951 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; 5-7 heavy chain; 5-7 light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 3 distinct chains · 18% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1077 | 21% helix, 31% strand | P0DTC2 |
| H, G, I | 5-7 heavy chain | protein | 134 | 7% helix, 37% strand | — |
| L, J, K | 5-7 light chain | protein | 106 | 3% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 60 copies · chains A, B, L, C, J, 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 | 1131 | 0.88 | 0.90 | 162 | empty |
| 2 | 899 | 0.84 | 0.86 | 105 | empty |
| 3 | 699 | 0.80 | 0.85 | 83 | empty |
| 4 | 894 | 0.79 | 0.81 | 76 | empty |
| 5 | 214 | 0.79 | 0.93 | 27 | empty |
Interfaces
18 interfaces between chains.
- B–C · 6533 Ų buried · 60 hydrogen bonds · protein-protein
- A–C · 6521 Ų buried · 57 hydrogen bonds · protein-protein
- A–B · 6510 Ų buried · 54 hydrogen bonds · protein-protein
- A–H · 1136 Ų buried · 15 hydrogen bonds · protein-protein
- B–G · 1133 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 glycan, 48 disulfide (N-glycosylation, disulfide).
Compared structures
- 7RW2 · Cryo-EM structure of NTD-directed neutralizing antibody 5-7 in complex with prefusion… · 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 7RW2 · PDBe 7RW2 · UniProt P0DTC2
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