MolNFT v1 · #105665 · protein

Crystal structure of human alpha-defensin 5, HD5 (THR7ARG GLU21ARG mutant)

4RBW · Defensin-5: “Crystal structure of human alpha-defensin 5, HD5 (THR7ARG GLU21ARG mutant)”. X-ray diffraction, 2 ligands (SO4, CL), 1 pocket (best druggability 0.30). MolNFT v1 #105665 on GenesisL1: 3D structure, binding sites and…

PDB: 4RBW
Type: protein
Length: 128 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Defensin-5
UniProt: Q01523
Ligands: SO4, CL
Pockets: 1 · best druggability 0.30

Structure

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

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

Ligands and binding sites

SO4 · Sulfate ion · ion · 9 copies · chains A, B, C, D
CL · Chloride ion · ion · 2 copies · chains B, C

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	74	0.30	0.73	19	SO4

Interfaces

4 interfaces between chains.

B–C · 476 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 420 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 192 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 95 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

4RBW · Crystal structure of human alpha-defensin 5, HD5 (Thr7Arg Glu21Arg mutant) · the same entry in another collection · chain D against D, 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 0.92

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 4RBW · PDBe 4RBW · UniProt Q01523

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