MolNFT v1 · #23623 · protein

Crystal structure of murine april, pH 8.0

1U5Y · Tumor necrosis factor ligand superfamily member 13: “Crystal structure of murine april, pH 8.0”. X-ray diffraction, 3 pockets (best druggability 0.60). MolNFT v1 #23623 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1U5Y
Type: protein
Length: 404 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tumor necrosis factor ligand superfamily member 13
UniProt: Q9D777
Pockets: 3 · best druggability 0.60

Structure

x-ray diffraction · 2 distinct chains · 1% helix, 58% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Tumor necrosis factor ligand superfamily member 13	protein	137	2% helix, 59% strand	Q9D777
D	Tumor necrosis factor ligand superfamily member 13	protein	130	0% helix, 58% strand	Q9D777

Pockets

3 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	223	0.60	0.81	29	empty
2	63	0.35	0.77	14	empty
3	56	0.32	0.76	13	empty

Interfaces

3 interfaces between chains.

A–B · 982 Å² buried · 17 hydrogen bonds · protein-protein
A–D · 891 Å² buried · 14 hydrogen bonds · protein-protein
B–D · 868 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

1U5Y · Crystal structure of murine APRIL, pH 8.0 · the same entry in another collection · chain A against A, TM-score 1.00
Q9D777 · AlphaFold monomer V2.0 prediction for tumor necrosis factor ligand superfamily member 13… · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q9D777
Elsewhere: RCSB PDB 1U5Y · PDBe 1U5Y · UniProt Q9D777

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