MolNFT v1 · #144826 · protein
An anti-GH/GL antibody that neutralizes dual-tropic infection defines a site of vulnerability on epstein-barr virus
6C5V · Envelope glycoprotein H: “An anti-GH/GL antibody that neutralizes dual-tropic infection defines a site of vulnerability on epstein-barr…”. Electron microscopy, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.77). MolNFT…
- PDB
- 6C5V
- Type
- protein
- Length
- 1,353 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein H; Envelope glycoprotein L; Glycoprotein 42; Antibody Fab AMMO1…
- UniProt
- K9US75, Q1HVF6, P0C6Z5
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.77
Structure
electron microscopy · 5 distinct chains · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein H | protein | 655 | 39% helix, 20% strand | K9US75 |
| B | Envelope glycoprotein L | protein | 94 | 41% helix, 15% strand | Q1HVF6 |
| C | Glycoprotein 42 | protein | 177 | 10% helix, 19% strand | P0C6Z5 |
| H | Antibody Fab AMMO1 heavy chain | protein | 215 | 8% helix, 53% strand | — |
| L | Antibody Fab AMMO1 light chain | protein | 212 | 9% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, C, B
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains L
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 868 | 0.77 | 0.80 | 83 | empty |
| 2 | 308 | 0.75 | 0.86 | 38 | empty |
| 3 | 194 | 0.72 | 0.88 | 34 | empty |
| 4 | 403 | 0.68 | 0.81 | 39 | empty |
| 5 | 355 | 0.65 | 0.79 | 47 | empty |
Interfaces
8 interfaces between chains.
- A–C · 2657 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1998 Ų buried · 19 hydrogen bonds · protein-protein
- H–L · 1662 Ų buried · 12 hydrogen bonds · protein-protein
- A–H · 499 Ų buried · 7 hydrogen bonds · protein-protein
- A–L · 302 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 9 glycan, 1 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 6C5V · An anti-gH/gL antibody that neutralizes dual-tropic infection defines a site of… · 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 K9US75
- Every structure of UniProt Q1HVF6
- Every structure of UniProt P0C6Z5
- Elsewhere: RCSB PDB 6C5V · PDBe 6C5V · UniProt K9US75 · UniProt Q1HVF6 · UniProt P0C6Z5
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