MolNFT v1 · #160952 · protein
MERS S0 trimer in complex with variable domain of antibody G2
6PZ8 · S protein: “MERS S0 trimer in complex with variable domain of antibody G2”. Electron microscopy, 3 ligands (NAG, BMA, MAN), 20 pockets (best druggability 0.86). MolNFT v1 #160952 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6PZ8
- Type
- protein
- Length
- 3,585 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S protein; G2 heavy chain; G2 light chain
- UniProt
- W5ZZF5, W6A090
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 4 distinct chains · 21% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I | S protein | protein | 463 | 41% helix, 19% strand | W5ZZF5 |
| B, J, F | S protein | protein | 513 | 9% helix, 41% strand | W6A090 |
| H, C, D | G2 heavy chain | protein | 116 | 10% helix, 54% strand | — |
| L, G, K | G2 light chain | protein | 103 | 3% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 66 copies · chains A, B, E, J, I, F
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains B, J, F
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains B, J, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 857 | 0.86 | 0.89 | 92 | empty |
| 2 | 995 | 0.86 | 0.87 | 99 | empty |
| 3 | 583 | 0.86 | 0.91 | 72 | empty |
| 4 | 1189 | 0.81 | 0.82 | 109 | empty |
| 5 | 511 | 0.80 | 0.87 | 52 | empty |
Interfaces
21 interfaces between chains.
- A–F · 1882 Ų buried · 28 hydrogen bonds · protein-protein
- B–E · 1881 Ų buried · 28 hydrogen bonds · protein-protein
- J–I · 1875 Ų buried · 28 hydrogen bonds · protein-protein
- E–I · 1592 Ų buried · 19 hydrogen bonds · protein-protein
- A–I · 1587 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 disulfide, 42 glycan (disulfide, N-glycosylation).
Compared structures
- 6PZ8 · MERS S0 trimer in complex with variable domain of antibody G2 · 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 W5ZZF5
- Every structure of UniProt W6A090
- Elsewhere: RCSB PDB 6PZ8 · PDBe 6PZ8 · UniProt W5ZZF5 · UniProt W6A090
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