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Crystal structure of april bound to a peptide

Analyse Crystal structure of april bound to a peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3K48
Type: protein
Length: 453 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tumor necrosis factor ligand superfamily member 13; Peptide
UniProt: Q9D777
Pockets: 5 · best druggability 0.58

Structure

x-ray diffraction · 3 distinct chains · 7% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Tumor necrosis factor ligand superfamily member 13	protein	137	0% helix, 61% strand	Q9D777
R	Peptide	protein	16	38% helix, 0% strand	—
S, T	Peptide	protein	13	46% helix, 0% strand	—

Pockets

5 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	117	0.58	0.85	23	empty
2	64	0.37	0.78	14	empty
3	74	0.35	0.76	14	empty
4	52	0.30	0.76	13	empty
5	52	0.28	0.75	12	empty

Interfaces

9 interfaces between chains.

B–D · 981 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 978 Å² buried · 18 hydrogen bonds · protein-protein
A–D · 954 Å² buried · 20 hydrogen bonds · protein-protein
D–R · 469 Å² buried · 5 hydrogen bonds · protein-protein
A–S · 463 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

3K48 · Crystal structure of APRIL bound to a peptide · the same entry in another collection · chain R against R, 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 3K48 · PDBe 3K48 · UniProt Q9D777

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