MolNFT v1 · #146608 · protein

Crystal structure of the G23A mutant of human alpha defensin HNP4.

6DMM · Neutrophil defensin 4: “Crystal structure of the G23A mutant of human alpha defensin HNP4.”. X-ray diffraction, 1 ligand (SO4), 11 pockets (best druggability 0.81). MolNFT v1 #146608 on GenesisL1: 3D structure, binding sites and…

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.

Pocket	Volume (Å³)	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 Å² buried · 3 hydrogen bonds · protein-protein
B–E · 379 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 373 Å² buried · 3 hydrogen bonds · protein-protein
G–H · 368 Å² buried · 6 hydrogen bonds · protein-protein
K–L · 354 Å² 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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