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Crystal structure of human defensin-5 R28A mutant.

Analyse Crystal structure of human defensin-5 R28A mutant. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5CUI
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: CL
Pockets: 2 · best druggability 0.59

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

CL · Chloride ion · ion · 11 copies · chains A, B, C, E, D, F
PG0 · 2-(2-methoxyethoxy)ethanol · additive · 4 copies · chains A, B, C, D, E, F
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains C, E, D
1PE · Pentaethylene glycol · additive · chains B, C, D

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

Pockets

2 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	306	0.59	0.77	37	1PE
2	112	0.41	0.76	25	MPD, CL

Interfaces

9 interfaces between chains.

B–C · 488 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 381 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 379 Å² buried · 12 hydrogen bonds · protein-protein
E–F · 374 Å² buried · 14 hydrogen bonds · protein-protein
D–F · 307 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 disulfide (disulfide).

Compared structures

5CUI · Crystal structure of Human Defensin-5 R28A mutant. · 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 0.89

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 5CUI · PDBe 5CUI · UniProt Q01523

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