GL1X · GenesisL1 explorer

MolNFT v1 · #111928 · protein + DNA

Hipb-O4 21MER complex

4Z5D · Antitoxin hipb: “Hipb-O4 21MER complex”. X-ray diffraction, 3 pockets (best druggability 0.51). MolNFT v1 #111928 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
4Z5D
Type
protein + DNA
Length
183 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Antitoxin hipb; DNA (5'- D(*TP*TP*TP*AP*TP*CP*CP*GP*CP*GP*AP*TP*CP*GP*CP*GP*GP*AP*TP*AP*A)…
UniProt
P23873
Pockets
3 · best druggability 0.51

Structure

x-ray diffraction · 3 distinct chains · 62% helix, 13% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, BAntitoxin hipbprotein7162% helix, 13% strandP23873
CDNA (5'- D(*TP*TP*TP*AP*TP*CP*CP*GP*CP*GP*AP*TP*CP*GP*CP*GP*GP*AP*TP*AP*A)- 3')dna21——
DDNA (5'- D(*TP*TP*TP*AP*TP*CP*CP*GP*CP*GP*AP*TP*CP*GP*CP*GP*GP*AP*TP*A)-3')dna20——

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11910.510.7819empty
21860.510.7817empty
31550.480.7824empty

Interfaces

6 interfaces between chains.

  • A–B · 1395 Ų buried · 24 hydrogen bonds · protein-protein
  • C–D · 865 Ų buried · 83 hydrogen bonds · nucleic-nucleic
  • A–C · 372 Ų buried · 9 hydrogen bonds · protein-nucleic
  • B–D · 368 Ų buried · 9 hydrogen bonds · protein-nucleic
  • B–C · 331 Ų buried · 8 hydrogen bonds · protein-nucleic

Compared structures

  • 4Z5D · HipB-O4 21mer complex · the same entry in another collection · chain B against B, TM-score 1.00
  • P23873 · AlphaFold monomer V2.0 prediction for antitoxin hipb (P23873) · a predicted model of the same protein · chain A against A, TM-score 0.96

Analyse

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