Research workbench
The 2019-ncov RBD/ACE2-B0AT1 complex
Analyse The 2019-ncov RBD/ACE2-B0AT1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6M17
- Type
- protein
- Length
- 3,072 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sodium-dependent neutral amino acid transporter B(0)AT1; Angiotensin-converting enzyme 2…
- EC
- 3.4.17.23, 3.4.17.-
- UniProt
- Q695T7, Q9BYF1, P0DTC2
- Ligands
- LEU, NAG, ZN
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 3 distinct chains · 52% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Sodium-dependent neutral amino acid transporter B(0)AT1 | protein | 605 | 60% helix, 2% strand | Q695T7 |
| B, D | Angiotensin-converting enzyme 2 (EC 3.4.17.23, 3.4.17.-) | protein | 748 | 54% helix, 7% strand | Q9BYF1 |
| E, F | Spike protein S1 | protein | 183 | 15% helix, 24% strand | P0DTC2 |
Ligands and binding sites
- LEU · Leucine · ligand · 2 copies · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 44 copies · chains A, B, E, C, D, F
- ZN · Zinc ion · metal · 2 copies · chains 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 812 | 0.79 | 0.82 | 70 | empty |
| 2 | 769 | 0.78 | 0.82 | 71 | empty |
| 3 | 1106 | 0.75 | 0.78 | 123 | empty |
| 4 | 67 | 0.71 | 0.97 | 17 | LEU |
| 5 | 58 | 0.71 | 0.98 | 16 | LEU |
Interfaces
5 interfaces between chains.
- B–D · 1376 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1323 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1317 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 932 Ų buried · 22 hydrogen bonds · protein-protein
- B–E · 925 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 glycan, 12 disulfide (N-glycosylation, disulfide).
Compared structures
- 6M17 · The 2019-nCoV RBD/ACE2-B0AT1 complex · the same entry in another collection · chain B against B, TM-score 1.00
- Q695T7 · AlphaFold monomer V2.0 prediction for sodium-dependent neutral amino acid transporter… · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q9BYF1 · AlphaFold monomer V2.0 prediction for angiotensin-converting enzyme 2 (Q9BYF1) · a predicted model of the same protein · chain B against A, TM-score 0.94
- 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 0.79
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 Q695T7
- Every structure of UniProt Q9BYF1
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 6M17 · PDBe 6M17 · UniProt Q695T7 · UniProt Q9BYF1 · UniProt P0DTC2
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