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Crystal structure of M. tuberculosis mazf-MT3 T52D-F62D mutant in complex with DNA

Analyse Crystal structure of M. tuberculosis mazf-MT3 T52D-F62D mutant in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
5HK3
Type
protein + DNA
Length
221 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Endoribonuclease MAZF6; DNA (5'-D(*AP*GP*UP*CP*UP*CP*CP*UP*UP*UP*C)-3')
EC
3.1.27.-
UniProt
P9WII3
Pockets
2 · best druggability 0.49

Structure

x-ray diffraction · 3 distinct chains · 26% helix, 36% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AEndoribonuclease MAZF6 (EC 3.1.27.-)protein11323% helix, 35% strandP9WII3
BEndoribonuclease MAZF6 (EC 3.1.27.-)protein10330% helix, 37% strandP9WII3
CDNA (5'-D(*AP*GP*UP*CP*UP*CP*CP*UP*UP*UP*C)-3')dna5——

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11490.490.7923empty
21780.460.7526empty

Interfaces

2 interfaces between chains.

  • A–B · 1208 Ų buried · 22 hydrogen bonds · protein-protein
  • B–C · 466 Ų buried · 16 hydrogen bonds · protein-nucleic

Compared structures

  • 5HK3 · Crystal structure of M. tuberculosis MazF-mt3 T52D-F62D mutant in complex with DNA · the same entry in another collection · chain A against A, TM-score 1.00
  • P9WII3 · AlphaFold monomer V2.0 prediction for endoribonuclease MAZF6 (P9WII3) · a predicted model of the same protein · chain B against A, TM-score 0.98

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