MolNFT v1 · #182599 · protein
Cryoem structure of neutralizing nanobody NB12 in complex with SARS- COV2 spike
7MY3 · Spike glycoprotein: “Cryoem structure of neutralizing nanobody NB12 in complex with SARS- COV2 spike”. Electron microscopy, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.87). MolNFT v1 #182599 on GenesisL1: 3D structure…
- PDB
- 7MY3
- Type
- protein
- Length
- 3,385 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Nanobody NB12
- UniProt
- P0DTC2
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 4 distinct chains · 23% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1001 | 24% helix, 31% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1008 | 23% helix, 31% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1016 | 23% helix, 30% strand | P0DTC2 |
| H, E, D | Nanobody NB12 | protein | 120 | 6% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 58 copies · chains A, C, B
- BMA · beta-D-mannopyranose · sugar · 5 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 | 863 | 0.87 | 0.89 | 94 | empty |
| 2 | 1127 | 0.86 | 0.87 | 122 | empty |
| 3 | 956 | 0.79 | 0.81 | 80 | empty |
| 4 | 735 | 0.76 | 0.81 | 81 | empty |
| 5 | 670 | 0.75 | 0.81 | 80 | empty |
Interfaces
8 interfaces between chains.
- A–B · 4181 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 3938 Ų buried · 25 hydrogen bonds · protein-protein
- C–B · 3804 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 950 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 913 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 disulfide, 40 glycan (disulfide, N-glycosylation).
Compared structures
- 7MY3 · CryoEM structure of neutralizing nanobody Nb12 in complex with SARS-CoV2 spike · 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 7MY3 · PDBe 7MY3 · UniProt P0DTC2
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