MolNFT v1 · #123094 · protein

Crystal structure of the HIGA2 antitoxin C-terminal domain

5J9I · Antitoxin IgA-2: “Crystal structure of the HIGA2 antitoxin C-terminal domain”. X-ray diffraction, 3 pockets (best druggability 0.59). MolNFT v1 #123094 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5J9I
Type: protein
Length: 539 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antitoxin IgA-2
UniProt: Q9KMA5
Pockets: 3 · best druggability 0.59

Structure

x-ray diffraction · 5 distinct chains · 67% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Antitoxin IgA-2	protein	67	66% helix, 0% strand	Q9KMA5
B, D, F, H	Antitoxin IgA-2	protein	68	66% helix, 4% strand	Q9KMA5
C	Antitoxin IgA-2	protein	69	65% helix, 0% strand	Q9KMA5
E	Antitoxin IgA-2	protein	66	67% helix, 0% strand	Q9KMA5
G	Antitoxin IgA-2	protein	65	69% helix, 0% strand	Q9KMA5

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	531	0.59	0.74	68	empty
2	436	0.56	0.73	70	empty
3	62	0.29	0.74	19	empty

Interfaces

13 interfaces between chains.

A–B · 956 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 938 Å² buried · 7 hydrogen bonds · protein-protein
E–F · 849 Å² buried · 9 hydrogen bonds · protein-protein
G–H · 835 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 617 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

5J9I · Crystal structure of the HigA2 antitoxin C-terminal domain · the same entry in another collection · chain H against H, TM-score 1.00
Q9KMA5 · AlphaFold monomer V2.0 prediction for antitoxin higa-2 (Q9KMA5) · a predicted model of the same protein · chain G against A, TM-score 0.97

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 Q9KMA5
Elsewhere: RCSB PDB 5J9I · PDBe 5J9I · UniProt Q9KMA5

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