Research workbench
Cryoem structure of rbd domain of COVID-19 in complex with legobody
Analyse Cryoem structure of rbd domain of COVID-19 in complex with legobody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RXD
- Type
- protein
- Length
- 1,148 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltodextrin-binding PROTEIN,IMMUNOGLOBULIN G-binding protein A,IMMUNOGLOBULIN G-binding…
- UniProt
- A0A4Z0THX4, P99134, P06654, P0DTC2
- Ligands
- GLC
- Pockets
- 11 · best druggability 0.74
Structure
electron microscopy · 5 distinct chains · 23% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Maltodextrin-binding PROTEIN,IMMUNOGLOBULIN G-binding protein A,IMMUNOGLOBULIN G-binding protein G | protein | 439 | 46% helix, 19% strand | A0A4Z0THX4, P99134, P06654 |
| H | FAB_8D3_2 heavy chain | protein | 207 | 3% helix, 52% strand | — |
| L | FAB_8D3_2 light chain | protein | 204 | 7% helix, 51% strand | — |
| N | NB_RBD | protein | 125 | 5% helix, 54% strand | — |
| R | Spike protein S1 | protein | 173 | 18% helix, 25% strand | P0DTC2 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 300 | 0.74 | 0.86 | 30 | GLC |
| 2 | 445 | 0.65 | 0.78 | 59 | empty |
| 3 | 567 | 0.61 | 0.74 | 60 | empty |
| 4 | 124 | 0.50 | 0.80 | 26 | empty |
| 5 | 96 | 0.47 | 0.81 | 29 | empty |
Interfaces
7 interfaces between chains.
- H–L · 1723 Ų buried · 14 hydrogen bonds · protein-protein
- N–R · 1102 Ų buried · 12 hydrogen bonds · protein-protein
- B–N · 657 Ų buried · 6 hydrogen bonds · protein-protein
- B–H · 624 Ų buried · 16 hydrogen bonds · protein-protein
- L–N · 605 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 7RXD · CryoEM structure of RBD domain of COVID-19 in complex with Legobody · the same entry in another collection · chain H against H, TM-score 1.00
- P06654 · AlphaFold monomer V2.0 prediction for immunoglobulin G-binding protein G (P06654) · a predicted model of the same protein · chain B against A, TM-score 0.19
- P99134 · AlphaFold monomer V2.0 prediction for immunoglobulin G-binding protein a (P99134) · a predicted model of the same protein · chain B against A, TM-score 0.17
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 A0A4Z0THX4
- Every structure of UniProt P99134
- Every structure of UniProt P06654
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 7RXD · PDBe 7RXD · UniProt A0A4Z0THX4 · UniProt P99134 · UniProt P06654 · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.