MolNFT v1 · #27783 · protein

The crystal structure of april bound to taci

1XU1 · Tumor necrosis factor ligand superfamily member 13: “The crystal structure of april bound to taci”. X-ray diffraction, 1 ligand (NI), 6 pockets (best druggability 0.57). MolNFT v1 #27783 on GenesisL1: 3D structure, binding sites and…

PDB: 1XU1
Type: protein
Length: 524 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tumor necrosis factor ligand superfamily member 13; Tumor necrosis factor receptor…
UniProt: Q9D777, O14836
Ligands: NI
Pockets: 6 · best druggability 0.57

Structure

x-ray diffraction · 4 distinct chains · 18% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Tumor necrosis factor ligand superfamily member 13	protein	137	0% helix, 64% strand	Q9D777
R	Tumor necrosis factor receptor superfamily member 13B	protein	38	37% helix, 21% strand	O14836
S	Tumor necrosis factor receptor superfamily member 13B	protein	36	42% helix, 22% strand	O14836
T	Tumor necrosis factor receptor superfamily member 13B	protein	39	38% helix, 21% strand	O14836

Ligands and binding sites

NI · Nickel (II) ion · metal · chains A, B, D

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

Pockets

6 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	194	0.57	0.81	25	empty
2	98	0.40	0.77	21	empty
3	83	0.39	0.77	13	empty
4	68	0.37	0.78	13	empty
5	81	0.37	0.76	15	empty

Interfaces

9 interfaces between chains.

B–D · 947 Å² buried · 17 hydrogen bonds · protein-protein
A–D · 939 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 927 Å² buried · 16 hydrogen bonds · protein-protein
A–R · 701 Å² buried · 9 hydrogen bonds · protein-protein
B–S · 688 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

1XU1 · The crystal structure of APRIL bound to TACI · the same entry in another collection · chain T against T, 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
O14836 · AlphaFold monomer V2.0 prediction for tumor necrosis factor receptor superfamily member… · a predicted model of the same protein · chain T against A, TM-score 0.78

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
Every structure of UniProt O14836
Elsewhere: RCSB PDB 1XU1 · PDBe 1XU1 · UniProt Q9D777 · UniProt O14836

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