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The crystal structure of almond hnl, PAHNL5 V317A, in complex with benzyl alcohol
Analyse The crystal structure of almond hnl, PAHNL5 V317A, in complex with benzyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 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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