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Crystal structure of NLRC4 reveals its autoinhibition mechanism

Analyse Crystal structure of NLRC4 reveals its autoinhibition mechanism in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4KXF
Type: protein
Length: 7,145 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nlr family card domain-containing protein 4
UniProt: Q3UP24
Ligands: ADP, SO4
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 8 distinct chains · 46% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
K	Nlr family card domain-containing protein 4	protein	904	46% helix, 15% strand	Q3UP24
B	Nlr family card domain-containing protein 4	protein	903	45% helix, 15% strand	Q3UP24
D	Nlr family card domain-containing protein 4	protein	900	46% helix, 15% strand	Q3UP24
F	Nlr family card domain-containing protein 4	protein	899	47% helix, 16% strand	Q3UP24
H	Nlr family card domain-containing protein 4	protein	898	46% helix, 15% strand	Q3UP24
L	Nlr family card domain-containing protein 4	protein	893	46% helix, 16% strand	Q3UP24
N	Nlr family card domain-containing protein 4	protein	882	47% helix, 15% strand	Q3UP24
P	Nlr family card domain-containing protein 4	protein	866	46% helix, 15% strand	Q3UP24

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 8 copies · chains K, B, D, F, H, L, N, P
SO4 · Sulfate ion · ion · 2 copies · chains B, N

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1054	0.89	0.91	124	ADP
2	740	0.87	0.90	89	ADP
3	1060	0.84	0.85	77	empty
4	1089	0.84	0.85	73	empty
5	1035	0.83	0.84	91	ADP

Interfaces

13 interfaces between chains.

B–F · 2060 Å² buried · 34 hydrogen bonds · protein-protein
H–L · 1964 Å² buried · 25 hydrogen bonds · protein-protein
D–F · 1029 Å² buried · 10 hydrogen bonds · protein-protein
B–H · 920 Å² buried · 17 hydrogen bonds · protein-protein
K–F · 910 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 modified (phosphorylation).

Compared structures

4KXF · Crystal structure of NLRC4 reveals its autoinhibition mechanism · the same entry in another collection · chain P against P, TM-score 1.00
Q3UP24 · AlphaFold monomer V2.0 prediction for nlr family card domain- containing protein 4… · a predicted model of the same protein · chain N against A, TM-score 0.87

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 Q3UP24
Elsewhere: RCSB PDB 4KXF · PDBe 4KXF · UniProt Q3UP24

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