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Crystal structure of the unphosphorylated receiver domain of desr in the active state

Analyse Crystal structure of the unphosphorylated receiver domain of desr in the active… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4LE2
Type: protein
Length: 522 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transcriptional regulatory protein desr
UniProt: O34723
Ligands: K, PO4
Pockets: 2 · best druggability 0.46

Structure

x-ray diffraction · 4 distinct chains · 41% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transcriptional regulatory protein desr	protein	132	43% helix, 23% strand	O34723
B	Transcriptional regulatory protein desr	protein	130	40% helix, 23% strand	O34723
C	Transcriptional regulatory protein desr	protein	134	42% helix, 22% strand	O34723
D	Transcriptional regulatory protein desr	protein	126	40% helix, 24% strand	O34723

Ligands and binding sites

K · Potassium ion · metal · 8 copies · chains A, B, C, D
PO4 · Phosphate ion · ion · 3 copies · chains A, B, C

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	131	0.46	0.78	20	K
2	98	0.35	0.74	25	empty

Interfaces

3 interfaces between chains.

A–B · 855 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 816 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 380 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

4LE2 · Crystal structure of the unphosphorylated receiver domain of DesR in the active state · the same entry in another collection · chain D against D, TM-score 1.00
O34723 · AlphaFold monomer V2.0 prediction for transcriptional regulatory protein desr (O34723) · a predicted model of the same protein · chain A 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 O34723
Elsewhere: RCSB PDB 4LE2 · PDBe 4LE2 · UniProt O34723

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