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Structural basis for the negative regulation of bacterial stress response by RseB

Analyse Structural basis for the negative regulation of bacterial stress response by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3M4W
Type: protein
Length: 1,264 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.3
Source: Escherichia coli
Molecule: Sigma-E factor regulatory protein rseB; Sigma-E factor negative regulatory protein
UniProt: P0AFX9, P0AFX7
Ligands: ZN
Pockets: 19 · best druggability 0.75

Structure

x-ray diffraction · resolution 2.3 · 6 distinct chains · 17% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Sigma-E factor regulatory protein rseB	protein	284	14% helix, 48% strand	P0AFX9
C	Sigma-E factor regulatory protein rseB	protein	276	13% helix, 49% strand	P0AFX9
D	Sigma-E factor regulatory protein rseB	protein	269	14% helix, 49% strand	P0AFX9
E, F	Sigma-E factor negative regulatory protein	protein	42	48% helix, 0% strand	P0AFX7
G	Sigma-E factor negative regulatory protein	protein	36	39% helix, 0% strand	P0AFX7
H	Sigma-E factor negative regulatory protein	protein	31	32% helix, 0% strand	P0AFX7

Ligands and binding sites

ZN · Zinc ion · metal · 6 copies · chains A, D, B, C, E, F

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

Pockets

19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	891	0.75	0.79	99	empty
2	136	0.75	0.94	39	empty
3	601	0.69	0.78	74	empty
4	177	0.66	0.86	34	empty
5	142	0.66	0.88	29	empty

Interfaces

14 interfaces between chains.

A–E · 2148 Å² buried · 33 hydrogen bonds · protein-protein
B–F · 2147 Å² buried · 31 hydrogen bonds · protein-protein
C–G · 1967 Å² buried · 18 hydrogen bonds · protein-protein
D–H · 1560 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 915 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

3M4W · Structural basis for the negative regulation of bacterial stress response by rseb · the same entry in another collection · chain H against H, TM-score 1.00
P0AFX9 · AlphaFold monomer V2.0 prediction for sigma-E factor regulatory protein rseb (P0AFX9) · a predicted model of the same protein · chain A against A, TM-score 1.00
P0AFX7 · AlphaFold monomer V2.0 prediction for anti-sigma-E factor rsea (P0AFX7) · a predicted model of the same protein · chain G against A, TM-score 0.51

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 P0AFX9
Every structure of UniProt P0AFX7
Elsewhere: RCSB PDB 3M4W · PDBe 3M4W · UniProt P0AFX9 · UniProt P0AFX7

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