Research workbench

Crystal structure of a SIGMA54-activator suggests the mechanism for the conformational switch necessary for SIGMA54 binding

Analyse Crystal structure of a SIGMA54-activator suggests the mechanism for the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1OJL
Type: protein
Length: 1,624 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transcriptional regulatory protein zrar
UniProt: P25852
Ligands: ATP, PO4
Pockets: 13 · best druggability 0.77

Structure

x-ray diffraction · 6 distinct chains · 47% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transcriptional regulatory protein zrar	protein	292	49% helix, 10% strand	P25852
B	Transcriptional regulatory protein zrar	protein	251	44% helix, 12% strand	P25852
C	Transcriptional regulatory protein zrar	protein	252	46% helix, 13% strand	P25852
D	Transcriptional regulatory protein zrar	protein	297	46% helix, 11% strand	P25852
E	Transcriptional regulatory protein zrar	protein	285	47% helix, 11% strand	P25852
F	Transcriptional regulatory protein zrar	protein	247	47% helix, 10% strand	P25852

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · chains E
PO4 · Phosphate ion · ion · 5 copies · chains A, B, C, D, F

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

Pockets

13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1079	0.77	0.79	113	PO4
2	879	0.77	0.80	93	PO4
3	1003	0.77	0.79	97	ATP
4	1012	0.74	0.77	103	empty
5	514	0.69	0.79	65	PO4

Interfaces

7 interfaces between chains.

B–C · 1038 Å² buried · 11 hydrogen bonds · protein-protein
E–F · 996 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 953 Å² buried · 13 hydrogen bonds · protein-protein
D–E · 944 Å² buried · 12 hydrogen bonds · protein-protein
B–E · 349 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

1OJL · Crystal structure of a sigma54-activator suggests the mechanism for the conformational… · the same entry in another collection · chain F against F, TM-score 1.00
P25852 · AlphaFold monomer V2.0 prediction for transcriptional regulatory protein zrar (P25852) · a predicted model of the same protein · chain F 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 P25852
Elsewhere: RCSB PDB 1OJL · PDBe 1OJL · UniProt P25852

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.