MolNFT v1 · #139132 · protein
Crystal structure of pseudorabies virus glycoprotein D
5X5W · Gd: “Crystal structure of pseudorabies virus glycoprotein D”. X-ray diffraction, 6 pockets (best druggability 0.55). MolNFT v1 #139132 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5X5W
- Type
- protein
- Length
- 680 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gd; Nectin-1
- UniProt
- G3G933, Q9GL76
- Pockets
- 6 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Gd | protein | 233 | 19% helix, 31% strand | G3G933 |
| B, D | Nectin-1 | protein | 107 | 3% helix, 56% strand | Q9GL76 |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 352 | 0.55 | 0.75 | 45 | empty |
| 2 | 211 | 0.55 | 0.78 | 44 | empty |
| 3 | 164 | 0.53 | 0.79 | 33 | empty |
| 4 | 179 | 0.46 | 0.75 | 34 | empty |
| 5 | 74 | 0.36 | 0.77 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1204 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1180 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 399 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
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 G3G933
- Every structure of UniProt Q9GL76
- Elsewhere: RCSB PDB 5X5W · PDBe 5X5W · UniProt G3G933 · UniProt Q9GL76
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