MolNFT v1 · #140961 · protein
Structure of the domain IV(D_IV) of pseudorabies virus glycoprotein B( prv gb)
5YS2 · Envelope glycoprotein B,ENVELOPE glycoprotein B: “Structure of the domain IV(D_IV) of pseudorabies virus glycoprotein B( prv gb)”. X-ray diffraction, 11 pockets (best druggability 0.73). MolNFT v1 #140961 on GenesisL1: 3D structure…
- PDB
- 5YS2
- Type
- protein
- Length
- 1,040 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein B,ENVELOPE glycoprotein B
- UniProt
- A0A0U3FH21, A0A1Q0AKY1
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 6 distinct chains · 22% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein B,ENVELOPE glycoprotein B | protein | 175 | 22% helix, 37% strand | A0A0U3FH21, A0A1Q0AKY1 |
| B | Envelope glycoprotein B,ENVELOPE glycoprotein B | protein | 169 | 22% helix, 37% strand | A0A0U3FH21, A0A1Q0AKY1 |
| C | Envelope glycoprotein B,ENVELOPE glycoprotein B | protein | 177 | 21% helix, 36% strand | A0A0U3FH21, A0A1Q0AKY1 |
| D | Envelope glycoprotein B,ENVELOPE glycoprotein B | protein | 174 | 22% helix, 36% strand | A0A0U3FH21, A0A1Q0AKY1 |
| E | Envelope glycoprotein B,ENVELOPE glycoprotein B | protein | 172 | 21% helix, 37% strand | A0A0U3FH21, A0A1Q0AKY1 |
| F | Envelope glycoprotein B,ENVELOPE glycoprotein B | protein | 173 | 22% helix, 33% strand | A0A0U3FH21, A0A1Q0AKY1 |
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 700 | 0.73 | 0.79 | 58 | empty |
| 2 | 112 | 0.71 | 0.92 | 15 | empty |
| 3 | 420 | 0.71 | 0.82 | 47 | empty |
| 4 | 536 | 0.71 | 0.80 | 48 | empty |
| 5 | 533 | 0.70 | 0.80 | 60 | empty |
Interfaces
10 interfaces between chains.
- A–C · 2027 Ų buried · 24 hydrogen bonds · protein-protein
- D–F · 1987 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1979 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 1966 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 1961 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 5YS2 · Structure of the domain IV(D_IV) of Pseudorabies virus glycoprotein B( PRV gB) · 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 A0A0U3FH21
- Every structure of UniProt A0A1Q0AKY1
- Elsewhere: RCSB PDB 5YS2 · PDBe 5YS2 · UniProt A0A0U3FH21 · UniProt A0A1Q0AKY1
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