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

Analyse Structure of the transcriptional repressor ATU1419 (vanr) from agrobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

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).

ChainMoleculeTypeResiduesSecondary structureUniProt
ATranscriptional regulator, gntr familyprotein23964% helix, 5% strandA9CJ36
BDNA (5'-D(*AP*TP*GP*TP*AP*TP*AP*CP*AP*T)-3')dna10——

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.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1590.290.7413empty

Interfaces

1 interface between chains.

  • A–B · 327 Ų 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

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