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Structure of karilysin catalytic mmp domain

Analyse Structure of karilysin catalytic mmp domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2XS3
Type: protein
Length: 340 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Karilysin protease; Peptide ala-phe-thr-ser
UniProt: D0EM77
Ligands: ZN
Pockets: 1 · best druggability 0.27

Structure

x-ray diffraction · 2 distinct chains · 27% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Karilysin protease	protein	166	28% helix, 19% strand	D0EM77
C, D	Peptide ala-phe-thr-ser	protein	4	0% helix, 25% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, C, B, D
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	51	0.27	0.74	12	empty

Interfaces

3 interfaces between chains.

A–C · 415 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 404 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 340 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

2XS3 · Structure of karilysin catalytic MMP domain · the same entry in another collection · chain A against A, TM-score 1.00
D0EM77 · AlphaFold monomer V2.0 prediction for karilysin (D0EM77) · a predicted model of the same protein · chain A 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 D0EM77
Elsewhere: RCSB PDB 2XS3 · PDBe 2XS3 · UniProt D0EM77

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