MolNFT v2 · #215268 · protein
Prefusion RSV F Bound to Lonafarnib and D25 Fab
8KG5 · Fusion glycoprotein F0,Fibritin: “Prefusion RSV F Bound to Lonafarnib and D25 Fab”. Electron microscopy at 3.17, 1 ligand (336), 20 pockets (best druggability 0.83). MolNFT v2 #215268 on GenesisL1: 3D structure, binding sites and…
- PDB
- 8KG5
- Type
- protein
- Length
- 1,577 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.17
- Source
- Enterobacteria phage T4; Homo sapiens; Human respiratory syncytial virus A…
- Molecule
- Fusion glycoprotein F0,Fibritin; D25 heavy chain; D25 light chain
- UniProt
- P03420, P10104
- Ligands
- 336
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · resolution 3.17 · 3 distinct chains · 22% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Fusion glycoprotein F0,Fibritin | protein | 449 | 31% helix, 29% strand | P03420, P10104 |
| D | D25 heavy chain | protein | 124 | 5% helix, 51% strand | — |
| E | D25 light chain | protein | 106 | 3% helix, 40% strand | — |
Ligands and binding sites
- 336 · 4-{2-[4-(3,10-dibromo-8-chloro-6,11-dihydro-5H-benzo[5,6]cyclohepta[1,2-b]pyridin-11-yl)piperidin-1-yl]-2-oxoethyl}piperidine-1-carboxamide · ligand · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1127 | 0.83 | 0.84 | 80 | empty |
| 2 | 1174 | 0.82 | 0.83 | 83 | 336 |
| 3 | 587 | 0.76 | 0.82 | 65 | empty |
| 4 | 780 | 0.75 | 0.80 | 69 | empty |
| 5 | 1086 | 0.74 | 0.77 | 79 | empty |
Interfaces
7 interfaces between chains.
- B–C · 2200 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 2181 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 2165 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 787 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 771 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
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 P03420
- Every structure of UniProt P10104
- Elsewhere: RCSB PDB 8KG5 · PDBe 8KG5 · UniProt P03420 · UniProt P10104
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