Research workbench
Crystal structure of human alpha-defensin 1 (HNP1) I20A/L25A mutant
Analyse Crystal structure of human alpha-defensin 1 (HNP1) I20A/L25A mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LBF
- Type
- protein
- Length
- 235 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutrophil defensin 1
- UniProt
- P59665
- Pockets
- 4 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F, G, H | Neutrophil defensin 1 | protein | 30 | 0% helix, 53% strand | P59665 |
| E | Neutrophil defensin 1 | protein | 25 | 0% helix, 40% strand | P59665 |
Ligands and binding sites
- GOL · Glycerol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 178 | 0.48 | 0.76 | 26 | empty |
| 2 | 148 | 0.46 | 0.76 | 23 | empty |
| 3 | 81 | 0.40 | 0.78 | 16 | empty |
| 4 | 85 | 0.32 | 0.73 | 20 | empty |
Interfaces
16 interfaces between chains.
- F–G · 357 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 349 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 339 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 299 Ų buried · 2 hydrogen bonds · protein-protein
- E–G · 292 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 4LBF · Crystal structure of HUMAN ALPHA-DEFENSIN 1 (HNP1) I20A/L25A mutant · the same entry in another collection · chain H against H, TM-score 1.00
- P59665 · AlphaFold monomer V2.0 prediction for neutrophil defensin 1 (P59665) · a predicted model of the same protein · chain B against A, TM-score 0.86
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 P59665
- Elsewhere: RCSB PDB 4LBF · PDBe 4LBF · UniProt P59665
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