Research workbench
Structure of human monoclonal antibody E317 Fab complex with HSV-2 gd
Analyse Structure of human monoclonal antibody E317 Fab complex with HSV-2 gd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3W9E
- Type
- protein
- Length
- 655 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein D; Antibody Fab heavy chain; Antibody Fab light chain
- UniProt
- Q69467
- Ligands
- NAG, BMA, MAN
- Pockets
- 9 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Envelope glycoprotein D | protein | 229 | 17% helix, 32% strand | Q69467 |
| A | Antibody Fab heavy chain | protein | 215 | 6% helix, 52% strand | — |
| B | Antibody Fab light chain | protein | 211 | 8% helix, 54% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains C
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 369 | 0.65 | 0.80 | 49 | empty |
| 2 | 64 | 0.57 | 0.90 | 21 | empty |
| 3 | 351 | 0.56 | 0.75 | 52 | empty |
| 4 | 67 | 0.44 | 0.82 | 24 | empty |
| 5 | 91 | 0.39 | 0.77 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1630 Ų buried · 14 hydrogen bonds · protein-protein
- C–A · 1052 Ų buried · 12 hydrogen bonds · protein-protein
- C–B · 259 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3W9E · Structure of Human Monoclonal Antibody E317 Fab Complex with HSV-2 gD · the same entry in another collection · chain C against C, 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 Q69467
- Elsewhere: RCSB PDB 3W9E · PDBe 3W9E · UniProt Q69467
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