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Crystal structure of human defensin-5 Y27A mutant crystal form 2.

Analyse Crystal structure of human defensin-5 Y27A mutant crystal form 2. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5CUJ
Type: protein
Length: 192 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Defensin-5
UniProt: Q01523
Ligands: CA, CL
Pockets: 4 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 0% helix, 63% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Defensin-5	protein	32	0% helix, 63% strand	Q01523

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains A, E, F, B, C, D
CL · Chloride ion · ion · 12 copies · chains A, B, E, C, D, F
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains C, F, 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	79	0.75	0.96	12	CL
2	204	0.55	0.79	30	empty
3	166	0.55	0.80	29	CL
4	172	0.54	0.79	27	CL

Interfaces

12 interfaces between chains.

A–C · 353 Å² buried · 2 hydrogen bonds · protein-protein
B–E · 343 Å² buried · 2 hydrogen bonds · protein-protein
D–F · 337 Å² buried · 2 hydrogen bonds · protein-protein
C–F · 287 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 286 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 disulfide (disulfide).

Compared structures

5CUJ · Crystal structure of Human Defensin-5 Y27A mutant crystal form 2. · the same entry in another collection · chain F against F, TM-score 1.00
Q01523 · AlphaFold monomer V2.0 prediction for defensin-5 (Q01523) · a predicted model of the same protein · chain A against A, TM-score 0.82

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 5CUJ · PDBe 5CUJ · UniProt Q01523

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