Research workbench

Impa metallopeptidase in complex with T-antigen

Analyse Impa metallopeptidase in complex with T-antigen in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5KDX
Type: protein
Length: 1,767 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Metallopeptidase
UniProt: Q9I5W4
Ligands: SER, A2G, GAL, ZN, PO4
Pockets: 17 · best druggability 0.65

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Metallopeptidase	protein	884	41% helix, 15% strand	Q9I5W4
B	Metallopeptidase	protein	883	41% helix, 15% strand	Q9I5W4

Ligands and binding sites

SER · Serine · ligand · 2 copies · chains A, B
A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 2 copies · chains A, B
GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
ZN · Zinc ion · metal · 2 copies · chains A, B
PO4 · Phosphate ion · ion · 5 copies · chains A, B
EDO · 1,2-ethanediol · additive · 26 copies · chains A, B

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

Pockets

17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	414	0.65	0.78	41	empty
2	375	0.64	0.79	40	empty
3	304	0.59	0.78	39	empty
4	277	0.58	0.78	40	empty
5	165	0.53	0.80	25	EDO

Interfaces

1 interface between chains.

A–B · 1038 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

5KDX · IMPa metallopeptidase in complex with T-antigen · the same entry in another collection · chain A against A, TM-score 1.00
Q9I5W4 · AlphaFold monomer V2.0 prediction for immunomodulating metalloprotease (Q9I5W4) · 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 Q9I5W4
Elsewhere: RCSB PDB 5KDX · PDBe 5KDX · UniProt Q9I5W4

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