Research workbench
Crystal structure of SARS-cov-2 spike rbd in complex with human monoclonal antibody AZD8895
Analyse Crystal structure of SARS-cov-2 spike rbd in complex with human monoclonal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L7D
- Type
- protein
- Length
- 630 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain of human monoclonal antibody Fab AZD8895; Light chain of human monoclonal…
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Heavy chain of human monoclonal antibody Fab AZD8895 | protein | 219 | 8% helix, 51% strand | — |
| L | Light chain of human monoclonal antibody Fab AZD8895 | protein | 215 | 7% helix, 50% strand | — |
| E | Spike protein S1 | protein | 196 | 16% helix, 30% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains E
- GOL · Glycerol · additive · 6 copies · chains H, L, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 461 | 0.61 | 0.76 | 53 | empty |
| 2 | 134 | 0.41 | 0.74 | 28 | empty |
| 3 | 90 | 0.40 | 0.77 | 21 | empty |
| 4 | 80 | 0.30 | 0.72 | 19 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1753 Ų buried · 19 hydrogen bonds · protein-protein
- H–E · 495 Ų buried · 8 hydrogen bonds · protein-protein
- L–E · 249 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7L7D · Crystal structure of SARS-CoV-2 spike RBD in complex with human monoclonal antibody… · the same entry in another collection · chain H against H, 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 P0DTC2
- Elsewhere: RCSB PDB 7L7D · PDBe 7L7D · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.