MolNFT v1 · #98245 · protein
Crystal structure of the receptor-binding domain from newly emerged middle east respiratory syndrome coronavirus
4L3N · S protein: “Crystal structure of the receptor-binding domain from newly emerged middle east respiratory syndrome…”. X-ray diffraction, 1 ligand (NAG), 4 pockets (best druggability 0.63). MolNFT v1 #98245 on GenesisL1: 3D structure…
- PDB
- 4L3N
- Type
- protein
- Length
- 419 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S protein
- UniProt
- M4SVE7
- Ligands
- NAG
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S protein | protein | 209 | 17% helix, 36% strand | M4SVE7 |
| B | S protein | protein | 210 | 18% helix, 36% strand | M4SVE7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 297 | 0.63 | 0.80 | 38 | EDO |
| 2 | 139 | 0.46 | 0.77 | 22 | empty |
| 3 | 89 | 0.40 | 0.77 | 18 | empty |
| 4 | 51 | 0.25 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 328 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4L3N · Crystal structure of the receptor-binding domain from newly emerged Middle East… · 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 M4SVE7
- Elsewhere: RCSB PDB 4L3N · PDBe 4L3N · UniProt M4SVE7
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