MolNFT v1 · #190516 · protein
Cryo-EM structure of SARS-cov-2 omicron spike protein (S-6P-rrar) in complex with human ACE2 ectodomain (two-rbd-up state)
7XCH · Spike glycoprotein: “Cryo-EM structure of SARS-cov-2 omicron spike protein (S-6P-rrar) in complex with human ACE2 ectodomain…”. Electron microscopy, 2 ligands (NAG, ZN), 20 pockets (best druggability 0.90). MolNFT v1 #190516 on…
- PDB
- 7XCH
- Type
- protein
- Length
- 4,381 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, ZN
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · 3 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Spike glycoprotein | protein | 1062 | 22% helix, 30% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1065 | 20% helix, 33% strand | P0DTC2 |
| D, E | Processed angiotensin-converting enzyme 2 | protein | 596 | 62% helix, 4% strand | Q9BYF1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 70 copies · chains A, C, B, D, E
- ZN · Zinc ion · metal · 2 copies · chains 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 | 1038 | 0.90 | 0.91 | 120 | empty |
| 2 | 1047 | 0.87 | 0.88 | 119 | empty |
| 3 | 816 | 0.83 | 0.86 | 86 | empty |
| 4 | 969 | 0.83 | 0.84 | 102 | empty |
| 5 | 960 | 0.77 | 0.79 | 81 | empty |
Interfaces
5 interfaces between chains.
- B–C · 4653 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 4468 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 4009 Ų buried · 28 hydrogen bonds · protein-protein
- C–E · 935 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 890 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide, 46 glycan (disulfide, N-glycosylation).
Compared structures
- 7XCH · Cryo-EM structure of SARS-CoV-2 Omicron spike protein (S-6P-RRAR) in complex with human… · the same entry in another collection · chain B against B, 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 D 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 D 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 7XCH · PDBe 7XCH · UniProt P0DTC2 · UniProt Q9BYF1
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