MolNFT v1 · #138138 · protein
MERS S ectodomain trimer in complex with variable domain of neutralizing antibody G4
5W9I · Spike glycoprotein: “MERS S ectodomain trimer in complex with variable domain of neutralizing antibody G4”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.83). MolNFT v1 #138138 on GenesisL1: 3D structure…
- PDB
- 5W9I
- Type
- protein
- Length
- 3,618 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; G4 vh; G4 vl
- UniProt
- W5ZZF5
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 20% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I | Spike glycoprotein | protein | 463 | 41% helix, 17% strand | W5ZZF5 |
| B, F, J | Spike glycoprotein | protein | 513 | 8% helix, 38% strand | W5ZZF5 |
| C, G, K | G4 vh | protein | 119 | 8% helix, 52% strand | — |
| D, H, L | G4 vl | protein | 111 | 3% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 63 copies · chains A, C, B, E, G, F, I, K, J
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 | 830 | 0.83 | 0.86 | 106 | empty |
| 2 | 880 | 0.83 | 0.85 | 90 | empty |
| 3 | 867 | 0.83 | 0.85 | 102 | empty |
| 4 | 847 | 0.80 | 0.83 | 91 | empty |
| 5 | 930 | 0.79 | 0.81 | 67 | empty |
Interfaces
21 interfaces between chains.
- B–I · 1832 Ų buried · 19 hydrogen bonds · protein-protein
- E–J · 1787 Ų buried · 22 hydrogen bonds · protein-protein
- A–F · 1774 Ų buried · 21 hydrogen bonds · protein-protein
- A–I · 1653 Ų buried · 18 hydrogen bonds · protein-protein
- E–I · 1642 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 glycan, 42 disulfide (disulfide, N-glycosylation, glycosylation).
Compared structures
- 5W9I · MERS S ectodomain trimer in complex with variable domain of neutralizing antibody G4 · 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
- Elsewhere: RCSB PDB 5W9I · PDBe 5W9I · UniProt W5ZZF5
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