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Crystal structure of the G23A mutant of human alpha defensin HNP4.
Analyse Crystal structure of the G23A mutant of human alpha defensin HNP4. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DMM
- Type
- protein
- Length
- 384 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutrophil defensin 4
- UniProt
- P12838
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 64% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, J | Neutrophil defensin 4 | protein | 33 | 0% helix, 64% strand | P12838 |
| B, D, F, G | Neutrophil defensin 4 | protein | 31 | 0% helix, 61% strand | P12838 |
| H, I, K, L | Neutrophil defensin 4 | protein | 32 | 0% helix, 66% strand | P12838 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 22 copies · chains A, D, B, K, I, E, F, G, H, L, C, J
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains B, E, H, C, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1196 | 0.81 | 0.82 | 103 | SO4 |
| 2 | 206 | 0.50 | 0.75 | 24 | MPD |
| 3 | 126 | 0.48 | 0.79 | 15 | empty |
| 4 | 116 | 0.48 | 0.79 | 16 | SO4 |
| 5 | 100 | 0.45 | 0.79 | 19 | SO4 |
Interfaces
28 interfaces between chains.
- B–K · 380 Ų buried · 3 hydrogen bonds · protein-protein
- B–E · 379 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 373 Ų buried · 3 hydrogen bonds · protein-protein
- G–H · 368 Ų buried · 6 hydrogen bonds · protein-protein
- K–L · 354 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide (disulfide).
Compared structures
- 6DMM · Crystal structure of the G23A mutant of human alpha defensin HNP4. · the same entry in another collection · chain L against L, 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 P12838
- Elsewhere: RCSB PDB 6DMM · PDBe 6DMM · UniProt P12838
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