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Crystal structure of 4-1BBL/4-1BB (C121S) complex in P21 space group

Analyse Crystal structure of 4-1BBL/4-1BB (C121S) complex in P21 space group in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6CU0
Type: protein
Length: 1,672 residues
Chains: 12
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: 13 · best druggability 0.78

Structure

x-ray diffraction · 12 distinct chains · 3% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tumor necrosis factor ligand superfamily member 9	protein	152	2% helix, 55% strand	P41273
B	Tumor necrosis factor ligand superfamily member 9	protein	147	2% helix, 56% strand	P41273
C	Tumor necrosis factor ligand superfamily member 9	protein	147	2% helix, 56% strand	P41273
D	Tumor necrosis factor ligand superfamily member 9	protein	147	2% helix, 56% strand	P41273
E	Tumor necrosis factor ligand superfamily member 9	protein	144	2% helix, 58% strand	P41273
F	Tumor necrosis factor ligand superfamily member 9	protein	151	2% helix, 55% strand	P41273
G	Tumor necrosis factor receptor superfamily member 9	protein	131	5% helix, 34% strand	Q07011
H	Tumor necrosis factor receptor superfamily member 9	protein	132	5% helix, 35% strand	Q07011
J	Tumor necrosis factor receptor superfamily member 9	protein	129	2% helix, 34% strand	Q07011
K	Tumor necrosis factor receptor superfamily member 9	protein	132	5% helix, 33% strand	Q07011
L	Tumor necrosis factor receptor superfamily member 9	protein	129	3% helix, 36% strand	Q07011
I	Tumor necrosis factor receptor superfamily member 9	protein	131	5% helix, 35% strand	Q07011

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains G, H

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

Pockets

13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1190	0.78	0.80	117	empty
2	672	0.77	0.82	51	empty
3	985	0.76	0.78	92	empty
4	854	0.74	0.78	90	empty
5	800	0.70	0.76	81	empty

Interfaces

16 interfaces between chains.

A–G · 803 Å² buried · 10 hydrogen bonds · protein-protein
D–I · 801 Å² buried · 8 hydrogen bonds · protein-protein
B–K · 798 Å² buried · 10 hydrogen bonds · protein-protein
F–J · 729 Å² buried · 10 hydrogen bonds · protein-protein
E–H · 726 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 59 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

6CU0 · Crystal structure of 4-1BBL/4-1BB (C121S) complex in P21 space group · the same entry in another collection · chain I against I, 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 6CU0 · PDBe 6CU0 · UniProt P41273 · UniProt Q07011

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