MolNFT v1 · #180671 · protein
Crystal structure of SARS-cov-2 spike rbd in complex with human monoclonal antibodies AZD8895 and AZD1061
7L7E · Heavy chain of human monoclonal antibody AZD8895: “Crystal structure of SARS-cov-2 spike rbd in complex with human monoclonal antibodies AZD8895 and AZD1061”. X-ray diffraction, 2 ligands (NAG, PO4), 20 pockets (best druggability…
- PDB
- 7L7E
- Type
- protein
- Length
- 4,318 residues
- Chains
- 20
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain of human monoclonal antibody AZD8895; Light chain of human monoclonal…
- UniProt
- P0DTC2
- Ligands
- NAG, PO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 12 distinct chains · 8% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heavy chain of human monoclonal antibody AZD8895 | protein | 219 | 8% helix, 49% strand | — |
| B, L | Light chain of human monoclonal antibody Fab AZD8895 | protein | 214 | 7% helix, 51% strand | — |
| C | Heavy chain of human monoclonal antibody Fab AZD1061 | protein | 236 | 6% helix, 45% strand | — |
| D, F, N, P | Light chain of human monoclonal antibody Fab AZD1061 | protein | 219 | 7% helix, 49% strand | — |
| E, O | Heavy chain of human monoclonal antibody Fab AZD1061 | protein | 234 | 10% helix, 46% strand | — |
| H | Heavy chain of human monoclonal antibody AZD8895 | protein | 218 | 7% helix, 50% strand | — |
| I | Heavy chain of human monoclonal antibody AZD8895 | protein | 218 | 8% helix, 52% strand | — |
| J, U | Light chain of human monoclonal antibody Fab AZD8895 | protein | 213 | 8% helix, 51% strand | — |
| M | Heavy chain of human monoclonal antibody Fab AZD1061 | protein | 235 | 4% helix, 46% strand | — |
| T | Heavy chain of human monoclonal antibody AZD8895 | protein | 217 | 6% helix, 50% strand | — |
| G | Spike protein S1 | protein | 195 | 16% helix, 27% strand | P0DTC2 |
| K, S, b | Spike protein S1 | protein | 194 | 14% helix, 30% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains G, K, S, b
- PO4 · Phosphate ion · ion · 8 copies · chains A, B, H, L, I, J, T, U
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 | 1038 | 0.78 | 0.80 | 97 | empty |
| 2 | 1033 | 0.75 | 0.78 | 119 | empty |
| 3 | 578 | 0.71 | 0.80 | 66 | empty |
| 4 | 645 | 0.69 | 0.77 | 73 | empty |
| 5 | 640 | 0.67 | 0.76 | 80 | empty |
Interfaces
44 interfaces between chains.
- M–N · 2058 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 2025 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 2006 Ų buried · 13 hydrogen bonds · protein-protein
- O–P · 2003 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1829 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 56 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 7L7E · Crystal structure of SARS-CoV-2 spike RBD in complex with human monoclonal antibodies… · the same entry in another collection · chain A against A, 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 7L7E · PDBe 7L7E · UniProt P0DTC2
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