MolNFT v1 · #90561 · protein

Crystal structure of light

4EN0 · Tumor necrosis factor ligand superfamily member 14: “Crystal structure of light”. X-ray diffraction, 2 ligands (NAG, PO4), 2 pockets (best druggability 0.34). MolNFT v1 #90561 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4EN0
Type: protein
Length: 432 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tumor necrosis factor ligand superfamily member 14
UniProt: O43557
Ligands: NAG, PO4
Pockets: 2 · best druggability 0.34

Structure

x-ray diffraction · 3 distinct chains · 4% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tumor necrosis factor ligand superfamily member 14	protein	145	8% helix, 54% strand	O43557
B	Tumor necrosis factor ligand superfamily member 14	protein	143	2% helix, 52% strand	O43557
C	Tumor necrosis factor ligand superfamily member 14	protein	144	2% helix, 53% strand	O43557

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
PO4 · Phosphate ion · ion · chains A, B
GOL · Glycerol · additive · chains A, B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	61	0.34	0.77	12	empty
2	50	0.30	0.76	16	empty

Interfaces

3 interfaces between chains.

A–B · 1242 Å² buried · 26 hydrogen bonds · protein-protein
A–C · 1160 Å² buried · 21 hydrogen bonds · protein-protein
B–C · 1046 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

4EN0 · Crystal structure of light · the same entry in another collection · chain A against A, TM-score 1.00
O43557 · AlphaFold monomer V2.0 prediction for tumor necrosis factor ligand superfamily member 14… · a predicted model of the same protein · chain B against A, TM-score 0.94

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 O43557
Elsewhere: RCSB PDB 4EN0 · PDBe 4EN0 · UniProt O43557

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