MolNFT v1 · #105416 · protein + DNA

Structure of glnr-DNA complex

4R4E · Hth-type transcriptional regulator glnr: “Structure of glnr-DNA complex”. X-ray diffraction, 2 pockets (best druggability 0.43). MolNFT v1 #105416 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4R4E
Type: protein + DNA
Length: 184 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hth-type transcriptional regulator glnr; DNA (5'-D(*AP*TP*TP*CP*TP*GP*AP*CP*A)-3'); DNA…
UniProt: P37582
Pockets: 2 · best druggability 0.43

Structure

x-ray diffraction · 4 distinct chains · 59% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Hth-type transcriptional regulator glnr	protein	84	56% helix, 8% strand	P37582
A	Hth-type transcriptional regulator glnr	protein	83	61% helix, 8% strand	P37582
D	DNA (5'-D(APTPTPCPTPGPAPCP*A)-3')	dna	9	—	—
E	DNA (5'-D(TPGPTPCPAPGPTPA)-3')	dna	8	—	—

Ligands and binding sites

CXS · 3-cyclohexyl-1-propylsulfonic acid · additive · chains A

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	163	0.43	0.75	21	empty
2	73	0.35	0.76	13	empty

Interfaces

4 interfaces between chains.

B–A · 454 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 366 Å² buried · 13 hydrogen bonds · protein-nucleic
D–E · 327 Å² buried · 28 hydrogen bonds · nucleic-nucleic
B–E · 232 Å² buried · 7 hydrogen bonds · protein-nucleic

Compared structures

4R4E · Structure of GlnR-DNA complex · the same entry in another collection · chain B against B, TM-score 1.00
P37582 · AlphaFold monomer V2.0 prediction for hth-type transcriptional regulator glnr (P37582) · 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 P37582
Elsewhere: RCSB PDB 4R4E · PDBe 4R4E · UniProt P37582

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