MolNFT v1 · #171593 · protein + DNA

Structure of the transcriptional repressor ATU1419 (vanr) from agrobacterium fabrum in complex a palindromic DNA (P6422 space group)

6ZAB · Transcriptional regulator, gntr family: “Structure of the transcriptional repressor ATU1419 (vanr) from agrobacterium fabrum in complex a palindromic…”. X-ray diffraction, 1 ligand (ZN), 1 pocket (best druggability 0.29). MolNFT v1…

PDB: 6ZAB
Type: protein + DNA
Length: 249 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transcriptional regulator, gntr family; DNA (5'-D(*AP*TP*GP*TP*AP*TP*AP*CP*AP*T)-3')
UniProt: A9CJ36
Ligands: ZN
Pockets: 1 · best druggability 0.29

Structure

x-ray diffraction · 2 distinct chains · 64% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transcriptional regulator, gntr family	protein	239	64% helix, 5% strand	A9CJ36
B	DNA (5'-D(APTPGPTPAPTPAPCPAPT)-3')	dna	10	—	—

Ligands and binding sites

ZN · Zinc ion · metal · chains A
CIT · Citric acid · additive · chains A
PEG · Di(hydroxyethyl)ether · additive · chains A
EDO · 1,2-ethanediol · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	59	0.29	0.74	13	empty

Interfaces

1 interface between chains.

A–B · 327 Å² buried · 8 hydrogen bonds · protein-nucleic

Compared structures

6ZAB · Structure of the transcriptional repressor Atu1419 (VanR) from agrobacterium fabrum in… · the same entry in another collection · chain A against A, TM-score 1.00

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 A9CJ36
Elsewhere: RCSB PDB 6ZAB · PDBe 6ZAB · UniProt A9CJ36

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