MolNFT v1 · #168209 · protein

Crystal structure of metacaspase 4 from arabidopsis

6W8S · Metacaspase-4: “Crystal structure of metacaspase 4 from arabidopsis”. X-ray diffraction, 1 ligand (SO4), 14 pockets (best druggability 0.74). MolNFT v1 #168209 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6W8S
Type: protein
Length: 1,438 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Metacaspase-4
EC: 3.4.22.-
UniProt: O64517
Ligands: SO4
Pockets: 14 · best druggability 0.74

Structure

x-ray diffraction · 4 distinct chains · 37% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Metacaspase-4 (EC 3.4.22.-)	protein	362	37% helix, 16% strand	O64517
B	Metacaspase-4 (EC 3.4.22.-)	protein	357	36% helix, 18% strand	O64517
C	Metacaspase-4 (EC 3.4.22.-)	protein	361	37% helix, 18% strand	O64517
D	Metacaspase-4 (EC 3.4.22.-)	protein	358	37% helix, 19% strand	O64517

Ligands and binding sites

SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D

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

Pockets

14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	801	0.74	0.79	75	SO4
2	858	0.73	0.78	73	empty
3	271	0.72	0.86	38	empty
4	338	0.71	0.84	46	empty
5	55	0.46	0.84	11	empty

Interfaces

2 interfaces between chains.

B–C · 723 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 437 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6W8S · Crystal structure of metacaspase 4 from Arabidopsis · the same entry in another collection · chain D against D, TM-score 1.00
O64517 · AlphaFold monomer V2.0 prediction for metacaspase-4 (O64517) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 O64517
Elsewhere: RCSB PDB 6W8S · PDBe 6W8S · UniProt O64517

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