MolNFT v1 · #180030 · protein
Crystal structure of SARS-cov-2 spike protein receptor-binding domain complexed with a pre-pandemic antibody S-E6 Fab
7KN4 · Spike protein S1: “Crystal structure of SARS-cov-2 spike protein receptor-binding domain complexed with a pre-pandemic antibody…”. X-ray diffraction, 1 ligand (NAG), 12 pockets (best druggability 0.66). MolNFT v1 #180030 on…
- PDB
- 7KN4
- Type
- protein
- Length
- 1,231 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; S-E6 Fab heavy chain; S-E6 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 12 · best druggability 0.66
Structure
x-ray diffraction · 5 distinct chains · 9% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 194 | 17% helix, 30% strand | P0DTC2 |
| B | Spike protein S1 | protein | 182 | 13% helix, 31% strand | P0DTC2 |
| H | S-E6 Fab heavy chain | protein | 217 | 5% helix, 51% strand | — |
| L, N | S-E6 Fab light chain | protein | 211 | 9% helix, 51% strand | — |
| M | S-E6 Fab heavy chain | protein | 216 | 5% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 662 | 0.66 | 0.76 | 80 | empty |
| 2 | 316 | 0.63 | 0.79 | 41 | empty |
| 3 | 309 | 0.60 | 0.78 | 44 | empty |
| 4 | 313 | 0.52 | 0.74 | 43 | empty |
| 5 | 157 | 0.51 | 0.79 | 30 | empty |
Interfaces
9 interfaces between chains.
- H–L · 1604 Ų buried · 12 hydrogen bonds · protein-protein
- M–N · 1604 Ų buried · 12 hydrogen bonds · protein-protein
- A–L · 596 Ų buried · 15 hydrogen bonds · protein-protein
- B–N · 554 Ų buried · 13 hydrogen bonds · protein-protein
- B–M · 343 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7KN4 · Crystal structure of SARS-CoV-2 spike protein receptor-binding domain complexed with a… · 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 7KN4 · PDBe 7KN4 · UniProt P0DTC2
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