MolNFT v1 · #11651 · protein + DNA

Crystal structure of a cooperative qacr-DNA complex

1JT0 · Qaca operator: “Crystal structure of a cooperative qacr-DNA complex”. X-ray diffraction, 1 ligand (SO4), 14 pockets (best druggability 0.74). MolNFT v1 #11651 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1JT0
Type: protein + DNA
Length: 805 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Qaca operator; Hypothetical transcriptional regulator in qaca 5'REGION
UniProt: P0A0N4
Ligands: SO4
Pockets: 14 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 77% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E, F	Qaca operator	dna	28	—	—
A, B, C	Hypothetical transcriptional regulator in qaca 5'REGION	protein	188	79% helix, 0% strand	P0A0N4
D	Hypothetical transcriptional regulator in qaca 5'REGION	protein	185	76% helix, 0% strand	P0A0N4

Ligands and binding sites

SO4 · Sulfate ion · ion · 5 copies · chains A, B, D, C

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

Pockets

14 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	308	0.74	0.86	37	empty
2	313	0.70	0.83	45	empty
3	105	0.61	0.87	23	empty
4	99	0.59	0.86	19	empty
5	470	0.58	0.75	32	empty

Interfaces

11 interfaces between chains.

A–C · 1605 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 1522 Å² buried · 3 hydrogen bonds · protein-protein
E–F · 1254 Å² buried · 122 hydrogen bonds · nucleic-nucleic
E–D · 374 Å² buried · 13 hydrogen bonds · protein-nucleic
F–C · 354 Å² buried · 12 hydrogen bonds · protein-nucleic

Compared structures

1JT0 · Crystal structure of a cooperative QacR-DNA complex · the same entry in another collection · chain D against D, TM-score 1.00
P0A0N4 · AlphaFold monomer V2.0 prediction for hth-type transcriptional regulator qacr (P0A0N4) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P0A0N4
Elsewhere: RCSB PDB 1JT0 · PDBe 1JT0 · UniProt P0A0N4

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