MolNFT v1 · #148833 · protein

Structure of human 4-1BB ligand

6FIB · Tumor necrosis factor ligand superfamily member 9: “Structure of human 4-1BB ligand”. X-ray diffraction, 3 pockets (best druggability 0.81). MolNFT v1 #148833 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6FIB
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 9; Tumor necrosis factor ligand…
UniProt: P41273, A8K008
Pockets: 3 · best druggability 0.81

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	146	4% helix, 56% strand	P41273
B	Tumor necrosis factor ligand superfamily member 9,4-1BBL - CH/CL fusion	protein	140	4% helix, 56% strand	P41273
C	Tumor necrosis factor ligand superfamily member 9, uncharacterized protein	protein	146	4% helix, 54% strand	P41273, A8K008

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	756	0.81	0.85	70	empty
2	124	0.45	0.78	25	empty
3	137	0.39	0.74	33	empty

Interfaces

3 interfaces between chains.

A–C · 751 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 728 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 725 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

6FIB · Structure of human 4-1BB ligand · 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 B against A, TM-score 0.96

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
Every structure of UniProt A8K008
Elsewhere: RCSB PDB 6FIB · PDBe 6FIB · UniProt P41273 · UniProt A8K008

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