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Crystal structure of the HIGB2 toxin in complex with NB6

Analyse Crystal structure of the HIGB2 toxin in complex with NB6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5JA9
Type: protein
Length: 446 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Toxin higb-2; Nanobody 6
UniProt: Q9KMA6
Ligands: SO4
Pockets: 3 · best druggability 0.72

Structure

x-ray diffraction · 4 distinct chains · 22% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Toxin higb-2	protein	101	39% helix, 27% strand	Q9KMA6
D	Toxin higb-2	protein	100	39% helix, 29% strand	Q9KMA6
A	Nanobody 6	protein	123	8% helix, 48% strand	—
B	Nanobody 6	protein	122	7% helix, 48% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 7 copies · chains C, D, A, B
EDO · 1,2-ethanediol · additive · chains C, A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1167	0.72	0.76	89	SO4
2	205	0.46	0.74	30	empty
3	54	0.26	0.73	14	EDO

Interfaces

5 interfaces between chains.

C–A · 731 Å² buried · 19 hydrogen bonds · protein-protein
D–B · 722 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 242 Å² buried · 1 hydrogen bond · protein-protein
C–D · 127 Å² buried · 0 hydrogen bonds · protein-protein
D–A · 19 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

5JA9 · Crystal structure of the HigB2 toxin in complex with Nb6 · the same entry in another collection · chain C against C, TM-score 1.00
Q9KMA6 · AlphaFold monomer V2.0 prediction for toxin higb-2 (Q9KMA6) · a predicted model of the same protein · chain D against A, TM-score 0.95

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 Q9KMA6
Elsewhere: RCSB PDB 5JA9 · PDBe 5JA9 · UniProt Q9KMA6

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