MolNFT v1 · #167506 · protein
A 2.8 ångström cryo-EM structure of a glycoprotein B-neutralizing antibody complex reveals a critical domain for herpesvirus fusion initiation
6VN1 · Human monoclonal antibody 93K variable light chain: “A 2.8 ångström cryo-EM structure of a glycoprotein B-neutralizing antibody complex reveals a critical domain…”. Electron microscopy, 20 pockets (best druggability 0.82). MolNFT v1…
- PDB
- 6VN1
- Type
- protein
- Length
- 2,454 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human monoclonal antibody 93K variable light chain; Human monoclonal antibody 93K…
- UniProt
- A0A1B1JGG9
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 3 distinct chains · 14% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, M, N | Human monoclonal antibody 93K variable light chain | protein | 106 | 0% helix, 24% strand | — |
| H, I, J | Human monoclonal antibody 93K variable heavy chain | protein | 128 | 5% helix, 30% strand | — |
| A, B, C | Envelope glycoprotein B | protein | 584 | 19% helix, 36% strand | A0A1B1JGG9 |
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1163 | 0.82 | 0.83 | 105 | empty |
| 2 | 94 | 0.78 | 0.98 | 25 | empty |
| 3 | 128 | 0.71 | 0.92 | 25 | empty |
| 4 | 586 | 0.71 | 0.80 | 72 | empty |
| 5 | 128 | 0.71 | 0.91 | 26 | empty |
Interfaces
12 interfaces between chains.
- A–C · 6666 Ų buried · 75 hydrogen bonds · protein-protein
- B–C · 6662 Ų buried · 78 hydrogen bonds · protein-protein
- A–B · 6658 Ų buried · 77 hydrogen bonds · protein-protein
- N–J · 926 Ų buried · 6 hydrogen bonds · protein-protein
- L–H · 920 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide (disulfide).
Compared structures
- 6VN1 · A 2.8 Angstrom Cryo-EM Structure of a Glycoprotein B-Neutralizing Antibody Complex… · 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 A0A1B1JGG9
- Elsewhere: RCSB PDB 6VN1 · PDBe 6VN1 · UniProt A0A1B1JGG9
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