MolNFT v1 · #171731 · protein
Crystal structure of receptor binding domain of SARS-cov-2 spike glycoprotein in complex with EY6A Fab
6ZER · Spike protein S1: “Crystal structure of receptor binding domain of SARS-cov-2 spike glycoprotein in complex with EY6A Fab”. X-ray diffraction, 2 ligands (NAG, PO4), 19 pockets (best druggability 0.71). MolNFT v1 #171731 on…
- PDB
- 6ZER
- Type
- protein
- Length
- 1,896 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; EY6A heavy chain; EY6A light chain
- UniProt
- P0DTC2
- Ligands
- NAG, PO4
- Pockets
- 19 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Spike protein S1 | protein | 197 | 11% helix, 28% strand | P0DTC2 |
| H, B | EY6A heavy chain | protein | 221 | 5% helix, 50% strand | — |
| L, C, G | EY6A light chain | protein | 215 | 7% helix, 52% strand | — |
| A, D | Spike protein S1 | protein | 196 | 11% helix, 29% strand | P0DTC2 |
| F | EY6A heavy chain | protein | 220 | 5% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains E, A, D
- PO4 · Phosphate ion · ion · 4 copies · chains L, C, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1150 | 0.71 | 0.75 | 107 | empty |
| 2 | 284 | 0.58 | 0.77 | 34 | empty |
| 3 | 230 | 0.56 | 0.78 | 29 | empty |
| 4 | 180 | 0.55 | 0.80 | 25 | empty |
| 5 | 203 | 0.55 | 0.78 | 26 | empty |
Interfaces
14 interfaces between chains.
- H–L · 2127 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 2078 Ų buried · 5 hydrogen bonds · protein-protein
- F–G · 2070 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 695 Ų buried · 7 hydrogen bonds · protein-protein
- D–F · 654 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6ZER · Crystal structure of receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex… · 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 6ZER · PDBe 6ZER · UniProt P0DTC2
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