Research workbench
MERS S ectodomain trimer in complex with variable domain of neutralizing antibody G4
Analyse MERS S ectodomain trimer in complex with variable domain of neutralizing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W9N
- Type
- protein
- Length
- 4,021 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MERS S; G4 vh; G4 vl
- UniProt
- W5ZZF5
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 5 distinct chains · 24% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | MERS S | protein | 463 | 40% helix, 18% strand | W5ZZF5 |
| B, E | G4 vh | protein | 119 | 8% helix, 54% strand | — |
| C, F | G4 vl | protein | 111 | 3% helix, 53% strand | — |
| G | MERS S | protein | 457 | 39% helix, 17% strand | W5ZZF5 |
| H, I, J | MERS S | protein | 726 | 11% helix, 37% strand | W5ZZF5 |
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 | 971 | 0.85 | 0.86 | 96 | empty |
| 2 | 1085 | 0.84 | 0.85 | 120 | empty |
| 3 | 1033 | 0.84 | 0.85 | 94 | empty |
| 4 | 1132 | 0.83 | 0.84 | 104 | empty |
| 5 | 1167 | 0.83 | 0.84 | 137 | empty |
Interfaces
18 interfaces between chains.
- A–J · 2064 Ų buried · 23 hydrogen bonds · protein-protein
- G–I · 2011 Ų buried · 22 hydrogen bonds · protein-protein
- D–H · 1726 Ų buried · 27 hydrogen bonds · protein-protein
- D–G · 1651 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1631 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 53 disulfide (disulfide).
Compared structures
- 5W9N · MERS S ectodomain trimer in complex with variable domain of neutralizing antibody G4 · the same entry in another collection · chain I against I, 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 5W9N · PDBe 5W9N · UniProt W5ZZF5
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