Research workbench
Pseudoatomic model of the pre-fusion conformation of glycoprotein B of herpes simplex virus 1
Analyse Pseudoatomic model of the pre-fusion conformation of glycoprotein B of herpes… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z9M
- Type
- protein
- Length
- 1,818 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein B
- UniProt
- A1Z0P7
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · 1 distinct chain · 18% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Envelope glycoprotein B | protein | 606 | 18% helix, 32% strand | A1Z0P7 |
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 922 | 0.90 | 0.93 | 148 | empty |
| 2 | 535 | 0.87 | 0.93 | 73 | empty |
| 3 | 526 | 0.83 | 0.89 | 68 | empty |
| 4 | 1054 | 0.82 | 0.83 | 104 | empty |
| 5 | 374 | 0.81 | 0.90 | 56 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3578 Ų buried · 76 hydrogen bonds · protein-protein
- A–C · 3234 Ų buried · 42 hydrogen bonds · protein-protein
- B–C · 3229 Ų buried · 56 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6Z9M · Pseudoatomic model of the pre-fusion conformation of glycoprotein B of Herpes simplex… · 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 A1Z0P7
- Elsewhere: RCSB PDB 6Z9M · PDBe 6Z9M · UniProt A1Z0P7
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