MolNFT v1 · #146612 · protein

Crystal structure of the T27A mutant of human alpha defensin HNP4.

6DMQ · Neutrophil defensin 4: “Crystal structure of the T27A mutant of human alpha defensin HNP4.”. X-ray diffraction, 3 pockets (best druggability 0.53). MolNFT v1 #146612 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6DMQ
Type: protein
Length: 255 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Neutrophil defensin 4
UniProt: P12838
Pockets: 3 · best druggability 0.53

Structure

x-ray diffraction · 3 distinct chains · 0% helix, 61% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Neutrophil defensin 4	protein	32	0% helix, 66% strand	P12838
B, D, F	Neutrophil defensin 4	protein	33	0% helix, 58% strand	P12838
C, E, G, H	Neutrophil defensin 4	protein	31	0% helix, 61% strand	P12838

Ligands and binding sites

MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	236	0.53	0.77	33	empty
2	77	0.39	0.78	20	empty
3	86	0.38	0.77	18	empty

Interfaces

11 interfaces between chains.

E–F · 332 Å² buried · 6 hydrogen bonds · protein-protein
G–H · 325 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 323 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 317 Å² buried · 4 hydrogen bonds · protein-protein
B–F · 197 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 disulfide (disulfide).

Compared structures

6DMQ · Crystal structure of the T27A mutant of human alpha defensin HNP4. · the same entry in another collection · chain H against H, TM-score 1.00
P12838 · AlphaFold monomer V2.0 prediction for neutrophil defensin 4 (P12838) · a predicted model of the same protein · chain H against A, TM-score 0.92

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 6DMQ · PDBe 6DMQ · UniProt P12838

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