MolNFT v1 · #117542 · protein
The crystal structure of almond hnl, PAHNL5 V317A, in complex with benzyl alcohol
5EB5 · Hnl isoenzyme 5: “The crystal structure of almond hnl, PAHNL5 V317A, in complex with benzyl alcohol”. X-ray diffraction, 3 ligands (FAD, 010, NAG), 6 pockets (best druggability 0.86). MolNFT v1 #117542 on GenesisL1: 3D structure…
- PDB
- 5EB5
- Type
- protein
- Length
- 1,018 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hnl isoenzyme 5
- UniProt
- Q7XJE8
- Ligands
- FAD, 010, NAG
- Pockets
- 6 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hnl isoenzyme 5 | protein | 509 | 28% helix, 27% strand | Q7XJE8 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- 010 · phenylmethanol · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 530 | 0.86 | 0.92 | 70 | FAD, 010 |
| 2 | 701 | 0.86 | 0.89 | 101 | FAD, 010 |
| 3 | 207 | 0.57 | 0.79 | 36 | empty |
| 4 | 262 | 0.51 | 0.75 | 39 | NAG |
| 5 | 58 | 0.33 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 181 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 5EB5 · The crystal structure of almond HNL, PaHNL5 V317A, in complex with benzyl alcohol · 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 5EB5 · PDBe 5EB5 · UniProt Q7XJE8
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