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Murine DR3 death domain

Analyse Murine DR3 death domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5YEV
Type: protein
Length: 1,812 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TNFRSF25 death domain
Ligands: SO4
Pockets: 13 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 50% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	TNFRSF25 death domain	protein	453	50% helix, 17% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 25 copies · chains A, C, B, D

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

Pockets

13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1016	0.81	0.82	91	SO4
2	936	0.79	0.81	68	SO4
3	1064	0.77	0.79	83	SO4
4	1196	0.76	0.79	95	SO4
5	471	0.60	0.75	48	empty

Interfaces

4 interfaces between chains.

B–D · 665 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 568 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 284 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 15 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5YEV · Murine DR3 death domain · the same entry in another collection · chain C against C, 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
Elsewhere: RCSB PDB 5YEV · PDBe 5YEV

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