MolNFT v1 · #138290 · protein
Crystal structure of HPVAL4
5WEE · Venom allergen like protein 4: “Crystal structure of HPVAL4”. X-ray diffraction, 2 ligands (NAG, FUC), 7 pockets (best druggability 0.78). MolNFT v1 #138290 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5WEE
- Type
- protein
- Length
- 749 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Venom allergen like protein 4
- UniProt
- A0A183GMB4
- Ligands
- NAG, FUC
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Venom allergen like protein 4 | protein | 188 | 32% helix, 23% strand | A0A183GMB4 |
| B, C, D | Venom allergen like protein 4 | protein | 187 | 32% helix, 23% strand | A0A183GMB4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B, D, C
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 646 | 0.78 | 0.83 | 52 | empty |
| 2 | 69 | 0.45 | 0.82 | 16 | empty |
| 3 | 87 | 0.41 | 0.78 | 16 | empty |
| 4 | 102 | 0.38 | 0.75 | 18 | empty |
| 5 | 61 | 0.30 | 0.74 | 17 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1081 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1004 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 485 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 174 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5WEE · Crystal structure of HpVAL4 · 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 A0A183GMB4
- Elsewhere: RCSB PDB 5WEE · PDBe 5WEE · UniProt A0A183GMB4
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