Research workbench

Caspase-4 P22/P10 C258A in complex with human gsdmd-C domain

Analyse Caspase-4 P22/P10 C258A in complex with human gsdmd-C domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6KMZ
Type: protein
Length: 1,341 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caspase-4; Gasdermin-D
EC: 3.4.22.57
UniProt: P49662, P57764
Pockets: 20 · best druggability 0.74

Structure

x-ray diffraction · 4 distinct chains · 49% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Caspase-4 (EC 3.4.22.57)	protein	173	28% helix, 24% strand	P49662
E	Gasdermin-D	protein	162	66% helix, 1% strand	P57764
H	Gasdermin-D	protein	135	69% helix, 1% strand	P57764
a, b, c, d	Caspase-4 (EC 3.4.22.57)	protein	88	27% helix, 24% strand	P49662

Pockets

20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	333	0.74	0.85	37	empty
2	364	0.74	0.85	32	empty
3	361	0.72	0.83	33	empty
4	140	0.55	0.82	20	empty
5	136	0.51	0.80	18	empty

Interfaces

19 interfaces between chains.

C–c · 3112 Å² buried · 60 hydrogen bonds · protein-protein
A–a · 3094 Å² buried · 59 hydrogen bonds · protein-protein
B–b · 2959 Å² buried · 55 hydrogen bonds · protein-protein
D–d · 2940 Å² buried · 50 hydrogen bonds · protein-protein
a–b · 1523 Å² buried · 31 hydrogen bonds · protein-protein

Compared structures

6KMZ · caspase-4 P22/P10 C258A in complex with human GSDMD-C domain · the same entry in another collection · chain d against d, TM-score 1.00
P49662 · AlphaFold monomer V2.0 prediction for caspase-4 (P49662) · a predicted model of the same protein · chain a 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 P49662
Every structure of UniProt P57764
Elsewhere: RCSB PDB 6KMZ · PDBe 6KMZ · UniProt P49662 · UniProt P57764

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