MolNFT v1 · #138137 · protein
MERS S ectodomain trimer in complex with variable domain of neutralizing antibody G4
5W9H: “MERS S ectodomain trimer in complex with variable domain of neutralizing antibody G4”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.87). MolNFT v1 #138137 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5W9H
- Type
- protein
- Length
- 4,257 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MERS S; G4 vh; G4 vl
- UniProt
- W5ZZF5
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 4 distinct chains · 19% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G | MERS S | protein | 463 | 40% helix, 18% strand | W5ZZF5 |
| B, E, H | G4 vh | protein | 119 | 8% helix, 54% strand | — |
| C, F, I | G4 vl | protein | 111 | 3% helix, 49% strand | — |
| p, q, r | MERS S | protein | 726 | 11% helix, 37% strand | W5ZZF5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 63 copies · chains A, B, D, E, G, H, p, q, r
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 | 1131 | 0.87 | 0.88 | 119 | empty |
| 2 | 1096 | 0.87 | 0.87 | 121 | empty |
| 3 | 511 | 0.83 | 0.90 | 61 | empty |
| 4 | 538 | 0.80 | 0.87 | 76 | empty |
| 5 | 493 | 0.80 | 0.87 | 84 | empty |
Interfaces
21 interfaces between chains.
- A–r · 2026 Ų buried · 26 hydrogen bonds · protein-protein
- G–q · 1969 Ų buried · 25 hydrogen bonds · protein-protein
- D–p · 1684 Ų buried · 25 hydrogen bonds · protein-protein
- D–G · 1546 Ų buried · 17 hydrogen bonds · protein-protein
- A–G · 1531 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 55 disulfide, 42 glycan (disulfide, N-glycosylation).
Compared structures
- 5W9H · 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 5W9H · PDBe 5W9H · UniProt W5ZZF5
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