MolNFT v1 · #189254 · protein
Cryo-EM structure of SARS-cov-2 S-delta variant (B.1.617.2), one rbd- up conformation 5
7V7S · Spike glycoprotein: “Cryo-EM structure of SARS-cov-2 S-delta variant (B.1.617.2), one rbd- up conformation 5”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.87). MolNFT v1 #189254 on GenesisL1: 3D structure…
- PDB
- 7V7S
- Type
- protein
- Length
- 3,088 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 21% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1027 | 21% helix, 32% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1033 | 21% helix, 31% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1028 | 21% helix, 33% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 81 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1057 | 0.87 | 0.88 | 128 | empty |
| 2 | 1116 | 0.87 | 0.88 | 110 | empty |
| 3 | 886 | 0.80 | 0.82 | 71 | empty |
| 4 | 952 | 0.80 | 0.81 | 103 | empty |
| 5 | 642 | 0.73 | 0.80 | 51 | empty |
Interfaces
3 interfaces between chains.
- A–C · 4327 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 4321 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 4088 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 glycan, 40 disulfide (N-glycosylation, disulfide).
Compared structures
- 7V7S · Cryo-EM structure of SARS-CoV-2 S-Delta variant (B.1.617.2), one RBD-up conformation 5 · 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 7V7S · PDBe 7V7S · UniProt P0DTC2
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