MolNFT v1 · #188047 · protein
Cryo-EM structure of SARS-cov-2 omicron spike protein in complex with human ACE2
7T9K · Spike glycoprotein: “Cryo-EM structure of SARS-cov-2 omicron spike protein in complex with human ACE2”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.87). MolNFT v1 #188047 on GenesisL1: 3D structure, binding…
- PDB
- 7T9K
- Type
- protein
- Length
- 4,087 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Processed angiotensin-converting enzyme 2
- UniProt
- P0DTC2, Q9BYF1
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Spike glycoprotein | protein | 1032 | 21% helix, 34% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 833 | 24% helix, 37% strand | P0DTC2 |
| D, E | Processed angiotensin-converting enzyme 2 | protein | 595 | 62% helix, 3% strand | Q9BYF1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 70 copies · chains A, B, C, D, E
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 | 746 | 0.87 | 0.91 | 93 | empty |
| 2 | 1106 | 0.86 | 0.87 | 143 | empty |
| 3 | 681 | 0.83 | 0.87 | 86 | empty |
| 4 | 451 | 0.77 | 0.85 | 50 | empty |
| 5 | 585 | 0.75 | 0.82 | 44 | empty |
Interfaces
5 interfaces between chains.
- A–B · 4569 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 4525 Ų buried · 43 hydrogen bonds · protein-protein
- A–C · 4336 Ų buried · 47 hydrogen bonds · protein-protein
- A–D · 958 Ų buried · 14 hydrogen bonds · protein-protein
- B–E · 957 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 52 glycan, 40 disulfide (N-glycosylation, disulfide).
Compared structures
- 7T9K · Cryo-EM structure of SARS-CoV-2 Omicron spike protein in complex with human ACE2 · the same entry in another collection · chain C against C, TM-score 1.00
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain E against A, TM-score 0.99
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain E against A, TM-score 0.99
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain E against A, TM-score 0.99
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain E against A, TM-score 0.99
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
- Every structure of UniProt Q9BYF1
- Elsewhere: RCSB PDB 7T9K · PDBe 7T9K · UniProt P0DTC2 · UniProt Q9BYF1
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