Research workbench
Cryo-EM structure of prefusion-stabilized rsv F (ds-CAV1) in complex with Fab AM14
Analyse Cryo-EM structure of prefusion-stabilized rsv F (ds-CAV1) in complex with Fab… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MPG
- Type
- protein
- Length
- 2,640 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fusion glycoprotein F0,ENVELOPE glycoprotein; AM14 Fab heavy chain; AM14 Fab light chain
- UniProt
- A0A0X8XQD7
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 3 distinct chains · 18% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Fusion glycoprotein F0,ENVELOPE glycoprotein | protein | 451 | 29% helix, 29% strand | A0A0X8XQD7 |
| F, H, D | AM14 Fab heavy chain | protein | 216 | 6% helix, 52% strand | — |
| G, I, E | AM14 Fab light chain | protein | 213 | 7% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B, C
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 | 954 | 0.81 | 0.83 | 68 | empty |
| 2 | 708 | 0.80 | 0.84 | 66 | empty |
| 3 | 401 | 0.76 | 0.86 | 80 | empty |
| 4 | 554 | 0.75 | 0.82 | 58 | empty |
| 5 | 315 | 0.73 | 0.85 | 36 | empty |
Interfaces
18 interfaces between chains.
- A–B · 2430 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 2396 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 2347 Ų buried · 23 hydrogen bonds · protein-protein
- H–I · 1799 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 1688 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7MPG · Cryo-EM structure of Prefusion-stabilized RSV F (DS-Cav1) in complex with Fab AM14 · 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 A0A0X8XQD7
- Elsewhere: RCSB PDB 7MPG · PDBe 7MPG · UniProt A0A0X8XQD7
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