MolNFT v1 · #153027 · protein
MERS-cov spike N-terminal domain and 7D10 scfv complex
6J11 · N-terminal domain of spike glycoprotein: “MERS-cov spike N-terminal domain and 7D10 scfv complex”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.76). MolNFT v1 #153027 on GenesisL1: 3D structure…
- PDB
- 6J11
- Type
- protein
- Length
- 1,709 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-terminal domain of spike glycoprotein; Vh of 7D10; Vl of 7D10
- UniProt
- A0A2D0YPK3
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | N-terminal domain of spike glycoprotein | protein | 336 | 9% helix, 41% strand | A0A2D0YPK3 |
| H | Vh of 7D10 | protein | 128 | 7% helix, 48% strand | — |
| L, E, G | Vl of 7D10 | protein | 111 | 3% helix, 51% strand | — |
| D, F | Vh of 7D10 | protein | 120 | 8% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 39 copies · chains A, H, L, B, F, G, C, E, D
- MAN · alpha-D-mannopyranose · sugar · 15 copies · chains H, A, F, B, D, C
- BMA · beta-D-mannopyranose · sugar · 7 copies · chains A, H, B, F, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 714 | 0.76 | 0.81 | 79 | empty |
| 2 | 58 | 0.73 | 0.98 | 19 | empty |
| 3 | 58 | 0.73 | 0.98 | 17 | empty |
| 4 | 55 | 0.70 | 0.97 | 17 | empty |
| 5 | 383 | 0.69 | 0.81 | 42 | empty |
Interfaces
12 interfaces between chains.
- H–L · 902 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 827 Ų buried · 5 hydrogen bonds · protein-protein
- F–G · 823 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 750 Ų buried · 6 hydrogen bonds · protein-protein
- B–F · 639 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 glycan, 17 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 6J11 · MERS-CoV spike N-terminal domain and 7D10 scFv complex · the same entry in another collection · chain F against F, 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 A0A2D0YPK3
- Elsewhere: RCSB PDB 6J11 · PDBe 6J11 · UniProt A0A2D0YPK3
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