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Crystal structure of the prefusion rsv F glycoprotein bound by human antibody AM14
Analyse Crystal structure of the prefusion rsv F glycoprotein bound by human antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MMN
- Type
- protein
- Length
- 2,649 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AM14 Fab light chain; Fusion glycoprotein F2; Fusion glycoprotein F1,FIBRITIN; AM14 Fab…
- UniProt
- P03420
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, E, G | AM14 Fab light chain | protein | 216 | 6% helix, 49% strand | — |
| A, C, J | Fusion glycoprotein F2 | protein | 72 | 31% helix, 35% strand | P03420 |
| B, I, K | Fusion glycoprotein F1,FIBRITIN | protein | 373 | 30% helix, 32% strand | P03420 |
| M, H, D | AM14 Fab heavy chain | protein | 222 | 8% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
- GOL · Glycerol · additive · chains G, K, M
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 | 812 | 0.81 | 0.84 | 65 | empty |
| 2 | 865 | 0.80 | 0.82 | 75 | empty |
| 3 | 637 | 0.76 | 0.82 | 67 | empty |
| 4 | 656 | 0.75 | 0.81 | 52 | empty |
| 5 | 554 | 0.73 | 0.81 | 53 | empty |
Interfaces
24 interfaces between chains.
- C–I · 4055 Ų buried · 77 hydrogen bonds · protein-protein
- J–K · 4026 Ų buried · 75 hydrogen bonds · protein-protein
- A–B · 4009 Ų buried · 75 hydrogen bonds · protein-protein
- G–M · 1912 Ų buried · 14 hydrogen bonds · protein-protein
- E–D · 1912 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7MMN · Crystal Structure of the Prefusion RSV F Glycoprotein bound by human antibody AM14 · the same entry in another collection · chain L against L, 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 P03420
- Elsewhere: RCSB PDB 7MMN · PDBe 7MMN · UniProt P03420
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