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Crystal structure of human alpha-defensin 5, HD5 (LEU29ABA mutant)

Analyse Crystal structure of human alpha-defensin 5, HD5 (LEU29ABA mutant) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4E86
Type: protein
Length: 285 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Defensin-5
UniProt: Q01523
Ligands: CL
Pockets: 4 · best druggability 0.45

Structure

x-ray diffraction · 2 distinct chains · 0% helix, 60% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, E, F, G	Defensin-5	protein	32	0% helix, 59% strand	Q01523
D, H, L	Defensin-5	protein	31	0% helix, 61% strand	Q01523

Ligands and binding sites

CL · Chloride ion · ion · 3 copies · chains B, C, F, H, 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	71	0.45	0.82	17	CL
2	58	0.34	0.77	14	empty
3	92	0.34	0.74	23	empty
4	86	0.32	0.73	15	empty

Interfaces

20 interfaces between chains.

A–B · 528 Å² buried · 13 hydrogen bonds · protein-protein
E–F · 494 Å² buried · 6 hydrogen bonds · protein-protein
G–H · 448 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 439 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 393 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 27 disulfide, 9 modified (disulfide, nonstandard).

Compared structures

4E86 · Crystal structure of human alpha-defensin 5, HD5 (Leu29Aba mutant) · the same entry in another collection · chain L against L, TM-score 1.00
Q01523 · AlphaFold monomer V2.0 prediction for defensin-5 (Q01523) · a predicted model of the same protein · chain L 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 Q01523
Elsewhere: RCSB PDB 4E86 · PDBe 4E86 · UniProt Q01523

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