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Crystal structure of human alpha-defensin 6 (H27W mutant)

Analyse Crystal structure of human alpha-defensin 6 (H27W mutant) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3QTE
Type: protein
Length: 128 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Defensin-6
UniProt: Q01524
Ligands: CL
Pockets: 1 · best druggability 0.53

Structure

x-ray diffraction · 1 distinct chain · 0% helix, 59% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Defensin-6	protein	32	0% helix, 59% strand	Q01524

Ligands and binding sites

CL · Chloride ion · ion · 2 copies · chains A, B
GOL · Glycerol · additive · chains B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	276	0.53	0.75	31	CL

Interfaces

5 interfaces between chains.

B–C · 433 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 269 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 230 Å² buried · 0 hydrogen bonds · protein-protein
C–D · 144 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 99 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

3QTE · Crystal structure of human alpha-defensin 6 (H27W mutant) · the same entry in another collection · chain D against D, TM-score 1.00
Q01524 · AlphaFold monomer V2.0 prediction for defensin-6 (Q01524) · a predicted model of the same protein · chain D against A, TM-score 0.94

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 Q01524
Elsewhere: RCSB PDB 3QTE · PDBe 3QTE · UniProt Q01524

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