MolNFT v1 · #117541 · protein
The crystal structure of almond hnl, PAHNL5 V317A, expressed in aspergillus niger
5EB4 · Hnl isoenzyme 5: “The crystal structure of almond hnl, PAHNL5 V317A, expressed in aspergillus niger”. X-ray diffraction, 2 ligands (FAD, NAG), 8 pockets (best druggability 0.87). MolNFT v1 #117541 on GenesisL1: 3D structure, binding…
- PDB
- 5EB4
- Type
- protein
- Length
- 1,024 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hnl isoenzyme 5
- UniProt
- Q7XJE8
- Ligands
- FAD, NAG
- Pockets
- 8 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hnl isoenzyme 5 | protein | 515 | 29% helix, 27% strand | Q7XJE8 |
| B | Hnl isoenzyme 5 | protein | 509 | 29% helix, 27% strand | Q7XJE8 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 860 | 0.87 | 0.89 | 98 | FAD |
| 2 | 707 | 0.86 | 0.89 | 95 | FAD |
| 3 | 214 | 0.60 | 0.81 | 33 | empty |
| 4 | 209 | 0.48 | 0.75 | 37 | empty |
| 5 | 94 | 0.35 | 0.74 | 23 | NAG |
Interfaces
1 interface between chains.
- A–B · 365 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 5EB4 · The crystal structure of almond HNL, PaHNL5 V317A, expressed in Aspergillus niger · 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 Q7XJE8
- Elsewhere: RCSB PDB 5EB4 · PDBe 5EB4 · UniProt Q7XJE8
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