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Structure of human 4-1BBL

Analyse Structure of human 4-1BBL in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6MGE
Type: protein
Length: 453 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tumor necrosis factor ligand superfamily member 9
UniProt: P41273
Ligands: PO4
Pockets: 6 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 4% helix, 55% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tumor necrosis factor ligand superfamily member 9	protein	154	2% helix, 54% strand	P41273
B	Tumor necrosis factor ligand superfamily member 9	protein	155	6% helix, 53% strand	P41273
C	Tumor necrosis factor ligand superfamily member 9	protein	144	4% helix, 58% strand	P41273

Ligands and binding sites

PO4 · Phosphate ion · ion · 5 copies · chains A, B, C
GOL · Glycerol · additive · chains A, B, C

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	756	0.77	0.81	63	GOL
2	226	0.48	0.75	41	PO4
3	132	0.44	0.77	27	empty
4	106	0.40	0.76	20	PO4
5	50	0.37	0.81	15	empty

Interfaces

3 interfaces between chains.

A–B · 792 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 786 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 753 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

6MGE · Structure of human 4-1BBL · the same entry in another collection · chain A against A, TM-score 1.00
P41273 · AlphaFold monomer V2.0 prediction for tumor necrosis factor ligand superfamily member 9… · a predicted model of the same protein · chain C against A, TM-score 0.95

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 P41273
Elsewhere: RCSB PDB 6MGE · PDBe 6MGE · UniProt P41273

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