MolNFT v1 · #142420 · protein

Complex structure of human 4-1BB and 4-1BBL

6A3V · Tumor necrosis factor ligand superfamily member 9: “Complex structure of human 4-1BB and 4-1BBL”. X-ray diffraction, 1 ligand (NAG), 20 pockets (best druggability 0.80). MolNFT v1 #142420 on GenesisL1: 3D structure, binding sites…

PDB: 6A3V
Type: protein
Length: 3,342 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tumor necrosis factor ligand superfamily member 9; Tumor necrosis factor receptor…
UniProt: P41273, Q07011
Ligands: NAG
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 19 distinct chains · 1% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, M, W	Tumor necrosis factor ligand superfamily member 9	protein	149	0% helix, 56% strand	P41273
B, P	Tumor necrosis factor receptor superfamily member 9	protein	138	4% helix, 30% strand	Q07011
C	Tumor necrosis factor ligand superfamily member 9	protein	150	0% helix, 53% strand	P41273
D, F, L	Tumor necrosis factor receptor superfamily member 9	protein	134	4% helix, 28% strand	Q07011
E	Tumor necrosis factor ligand superfamily member 9	protein	148	0% helix, 55% strand	P41273
G	Tumor necrosis factor ligand superfamily member 9	protein	150	0% helix, 55% strand	P41273
H	Tumor necrosis factor receptor superfamily member 9	protein	131	0% helix, 30% strand	Q07011
I	Tumor necrosis factor ligand superfamily member 9	protein	145	0% helix, 57% strand	P41273
J	Tumor necrosis factor receptor superfamily member 9	protein	119	3% helix, 31% strand	Q07011
K	Tumor necrosis factor ligand superfamily member 9	protein	150	0% helix, 53% strand	P41273
N	Tumor necrosis factor receptor superfamily member 9	protein	133	3% helix, 26% strand	Q07011
O	Tumor necrosis factor ligand superfamily member 9	protein	147	0% helix, 54% strand	P41273
Q	Tumor necrosis factor ligand superfamily member 9	protein	147	0% helix, 56% strand	P41273
R	Tumor necrosis factor receptor superfamily member 9	protein	119	0% helix, 20% strand	Q07011
S	Tumor necrosis factor ligand superfamily member 9	protein	148	0% helix, 55% strand	P41273
T	Tumor necrosis factor receptor superfamily member 9	protein	127	0% helix, 22% strand	Q07011
U	Tumor necrosis factor ligand superfamily member 9	protein	147	0% helix, 53% strand	P41273
V	Tumor necrosis factor receptor superfamily member 9	protein	124	0% helix, 24% strand	Q07011
X	Tumor necrosis factor receptor superfamily member 9	protein	132	0% helix, 23% strand	Q07011

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains B, D, F, H, J, L, N, P, R, T, V, X

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

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	903	0.80	0.82	74	empty
2	623	0.80	0.85	53	empty
3	561	0.79	0.85	51	empty
4	649	0.78	0.83	50	empty
5	1126	0.78	0.80	131	empty

Interfaces

43 interfaces between chains.

K–L · 888 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 884 Å² buried · 13 hydrogen bonds · protein-protein
E–F · 874 Å² buried · 11 hydrogen bonds · protein-protein
W–X · 864 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 859 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 116 disulfide, 12 glycan (disulfide, N-glycosylation).

Compared structures

6A3V · Complex structure of human 4-1BB and 4-1BBL · the same entry in another collection · chain K against K, TM-score 1.00

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 Q07011
Elsewhere: RCSB PDB 6A3V · PDBe 6A3V · UniProt P41273 · UniProt Q07011

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