Research workbench
SARS-cov-2 spike in complex with AHB2-2GS-SB175
Analyse SARS-cov-2 spike in complex with AHB2-2GS-SB175 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UHC
- Type
- protein
- Length
- 3,192 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Multivalent miniprotein inhibitor AHB2-2GS-SB175
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 2 distinct chains · 26% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Spike glycoprotein | protein | 989 | 22% helix, 33% strand | P0DTC2 |
| K, C, E | Multivalent miniprotein inhibitor AHB2-2GS-SB175 | protein | 75 | 84% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 60 copies · chains A, B, D
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 | 942 | 0.87 | 0.89 | 105 | empty |
| 2 | 1119 | 0.86 | 0.87 | 125 | empty |
| 3 | 1005 | 0.77 | 0.79 | 108 | empty |
| 4 | 921 | 0.77 | 0.79 | 99 | empty |
| 5 | 161 | 0.73 | 0.91 | 36 | empty |
Interfaces
6 interfaces between chains.
- B–D · 3921 Ų buried · 36 hydrogen bonds · protein-protein
- A–D · 3914 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 3902 Ų buried · 36 hydrogen bonds · protein-protein
- D–E · 208 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 207 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 glycan, 39 disulfide (N-glycosylation, disulfide).
Compared structures
- 7UHC · SARS-CoV-2 spike in complex with AHB2-2GS-SB175 · 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 7UHC · PDBe 7UHC · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.