Research workbench
Crystal structure of a tgev coronavirus spike fragment in complex with the tgev neutralizing monoclonal antibody 1AF10
Analyse Crystal structure of a tgev coronavirus spike fragment in complex with the tgev… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4F2M
- Type
- protein
- Length
- 1,154 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Monoclonal antibody 1AF10, heavy chain; Monoclonal antibody 1AF10, light chain; Spike…
- UniProt
- Q0PKZ5
- Ligands
- NAG
- Pockets
- 13 · best druggability 0.51
Structure
x-ray diffraction · 5 distinct chains · 4% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Monoclonal antibody 1AF10, heavy chain | protein | 214 | 6% helix, 49% strand | — |
| B | Monoclonal antibody 1AF10, light chain | protein | 213 | 4% helix, 45% strand | — |
| C | Monoclonal antibody 1AF10, heavy chain | protein | 220 | 3% helix, 46% strand | — |
| D | Monoclonal antibody 1AF10, light chain | protein | 211 | 5% helix, 51% strand | — |
| E, F | Spike protein | protein | 148 | 2% helix, 51% strand | Q0PKZ5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains E, F
- ACY · Acetic acid · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 152 | 0.51 | 0.79 | 21 | empty |
| 2 | 256 | 0.51 | 0.75 | 41 | empty |
| 3 | 186 | 0.50 | 0.77 | 33 | empty |
| 4 | 267 | 0.49 | 0.74 | 41 | empty |
| 5 | 109 | 0.46 | 0.79 | 28 | empty |
Interfaces
7 interfaces between chains.
- C–D · 1652 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1651 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 520 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 487 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 445 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 4F2M · Crystal structure of a TGEV coronavirus Spike fragment in complex with the TGEV… · 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 Q0PKZ5
- Elsewhere: RCSB PDB 4F2M · PDBe 4F2M · UniProt Q0PKZ5
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