MolNFT v1 · #191404 · protein
Cryo-EM structure of SARS-cov-2 beta (B.1.351) spike protein in complex with human ACE2
8DLM · Spike glycoprotein: “Cryo-EM structure of SARS-cov-2 beta (B.1.351) spike protein in complex with human ACE2”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.87). MolNFT v1 #191404 on GenesisL1: 3D structure…
- PDB
- 8DLM
- Type
- protein
- Length
- 3,303 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Processed angiotensin-converting enzyme 2
- EC
- 3.4.17.23
- UniProt
- P0DTC2, Q9BYF1
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 4 distinct chains · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 837 | 24% helix, 36% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1034 | 21% helix, 34% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 836 | 24% helix, 36% strand | P0DTC2 |
| E | Processed angiotensin-converting enzyme 2 (EC 3.4.17.23) | protein | 596 | 62% helix, 4% strand | Q9BYF1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 62 copies · chains A, B, C, 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 | 1165 | 0.87 | 0.88 | 139 | empty |
| 2 | 129 | 0.76 | 0.95 | 24 | empty |
| 3 | 349 | 0.75 | 0.86 | 53 | empty |
| 4 | 524 | 0.75 | 0.83 | 43 | empty |
| 5 | 558 | 0.73 | 0.81 | 41 | empty |
Interfaces
4 interfaces between chains.
- B–C · 4450 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 4188 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 4132 Ų buried · 36 hydrogen bonds · protein-protein
- B–E · 928 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 glycan, 36 disulfide (N-glycosylation, disulfide).
Compared structures
- 8DLM · Cryo-EM structure of SARS-CoV-2 Beta (B.1.351) spike protein in complex with human ACE2 · the same entry in another collection · chain A against A, 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
- Q9BYF1 · AlphaFold monomer V2.0 prediction for angiotensin-converting enzyme 2 (Q9BYF1) · 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 0.98
- 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 0.98
- 3SCK · 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 0.98
- 3SCK · 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 0.98
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 8DLM · PDBe 8DLM · UniProt P0DTC2 · UniProt Q9BYF1
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