Research workbench

Methylated shigella flexneri mxic

Analyse Methylated shigella flexneri mxic in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2VIX
Type: protein
Length: 847 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein mxic
UniProt: Q04640
Pockets: 10 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 72% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Protein mxic	protein	283	72% helix, 0% strand	Q04640
C	Protein mxic	protein	281	73% helix, 0% strand	Q04640

Ligands and binding sites

GOL · Glycerol · additive · 2 copies · chains A, B
ACT · Acetate ion · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	877	0.76	0.79	82	empty
2	1113	0.72	0.75	56	empty
3	449	0.67	0.79	56	empty
4	61	0.46	0.83	16	empty
5	64	0.36	0.78	12	empty

Interfaces

3 interfaces between chains.

B–C · 811 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 521 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 362 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 60 modified (methylation).

Compared structures

2VIX · Methylated Shigella flexneri MxiC · the same entry in another collection · chain A against A, TM-score 1.00
Q04640 · AlphaFold monomer V2.0 prediction for protein mxic (Q04640) · 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 Q04640
Elsewhere: RCSB PDB 2VIX · PDBe 2VIX · UniProt Q04640

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