Research workbench
SARS-cov-2 omicron rbd in complex with human ACE2 and S304 Fab and S309 Fab
Analyse SARS-cov-2 omicron rbd in complex with human ACE2 and S304 Fab and S309 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TN0
- Type
- protein
- Length
- 3,269 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S309 light chain; S309 heavy chain; Angiotensin-converting enzyme 2; S304 Fab light…
- UniProt
- Q9BYF1, P0DTC2
- Ligands
- NAG, ZN, CL
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 11 distinct chains · 31% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S309 light chain | protein | 213 | 8% helix, 50% strand | — |
| B | S309 heavy chain | protein | 228 | 8% helix, 51% strand | — |
| C | S309 heavy chain | protein | 224 | 7% helix, 52% strand | — |
| D | S309 light chain | protein | 214 | 7% helix, 50% strand | — |
| E | Angiotensin-converting enzyme 2 | protein | 591 | 64% helix, 4% strand | Q9BYF1 |
| F | Angiotensin-converting enzyme 2 | protein | 547 | 68% helix, 3% strand | Q9BYF1 |
| G, N | S304 Fab light chain | protein | 214 | 7% helix, 52% strand | — |
| H | S304 Fab heavy chain | protein | 215 | 9% helix, 56% strand | — |
| I | Spike protein S1 | protein | 198 | 17% helix, 30% strand | P0DTC2 |
| M | S304 Fab heavy chain | protein | 214 | 9% helix, 55% strand | — |
| S | Spike protein S1 | protein | 197 | 16% helix, 30% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains E, H, F, A, B, I, C, D, S
- ZN · Zinc ion · metal · 2 copies · chains E, F
- CL · Chloride ion · ion · 21 copies · chains A, B, C, D, S, E, F, I, N
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B, G, N, M, S
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1182 | 0.82 | 0.83 | 136 | empty |
| 2 | 146 | 0.70 | 0.89 | 27 | empty |
| 3 | 730 | 0.69 | 0.76 | 81 | empty |
| 4 | 1161 | 0.69 | 0.74 | 111 | EDO |
| 5 | 471 | 0.68 | 0.79 | 44 | empty |
Interfaces
16 interfaces between chains.
- G–H · 1748 Ų buried · 11 hydrogen bonds · protein-protein
- M–N · 1687 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1652 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1644 Ų buried · 11 hydrogen bonds · protein-protein
- E–I · 909 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 29 disulfide, 11 glycan (disulfide, N-glycosylation).
Compared structures
- 7TN0 · SARS-CoV-2 Omicron RBD in complex with human ACE2 and S304 Fab and S309 Fab · the same entry in another collection · chain I against I, 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 Q9BYF1
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 7TN0 · PDBe 7TN0 · UniProt Q9BYF1 · UniProt P0DTC2
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