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Crystal structure of the STX2A complexed with mma betaala peptide

Analyse Crystal structure of the STX2A complexed with mma betaala peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7D6R
Type: protein
Length: 635 residues
Chains: 7
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RRNA N-glycosylase; Shiga toxin 2 B subunit; Mma betaala peptide
EC: 3.2.2.22
UniProt: Q8XBV2, Q7DJJ2
Ligands: 1PS, NH2
Pockets: 3 · best druggability 0.70

Structure

x-ray diffraction · 4 distinct chains · 31% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RRNA N-glycosylase (EC 3.2.2.22)	protein	282	39% helix, 24% strand	Q8XBV2
B, E	Shiga toxin 2 B subunit	protein	69	16% helix, 48% strand	Q7DJJ2
C, D, F	Shiga toxin 2 B subunit	protein	70	16% helix, 49% strand	Q7DJJ2
G	Mma betaala peptide	protein	5	0% helix, 20% strand	—

Ligands and binding sites

1PS · 3-pyridinium-1-ylpropane-1-sulfonate · ligand · 4 copies · chains B, C, D, E, F
NH2 · Amino group · ion · chains A, G

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

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	251	0.70	0.85	32	empty
2	198	0.51	0.77	28	empty
3	163	0.45	0.75	36	empty

Interfaces

12 interfaces between chains.

D–E · 766 Å² buried · 14 hydrogen bonds · protein-protein
E–F · 757 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 743 Å² buried · 15 hydrogen bonds · protein-protein
B–F · 731 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 717 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

7D6R · Crystal structure of the Stx2a complexed with MMA betaAla peptide · the same entry in another collection · chain A against A, TM-score 1.00

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 Q8XBV2
Every structure of UniProt Q7DJJ2
Elsewhere: RCSB PDB 7D6R · PDBe 7D6R · UniProt Q8XBV2 · UniProt Q7DJJ2

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