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MolNFT v1 · #18085 · protein + DNA

Crystal structure of a paired domain-DNA complex at 2.5 ångströms resolution reveals structural basis for pax developmental mutations

1PDN · DNA (5'- D(*AP*AP*CP*GP*TP*CP*AP*CP*GP*GP*TP*TP*GP*AP*C)-3'): “Crystal structure of a paired domain-DNA complex at 2.5 ångströms resolution reveals structural basis for pax…”. X-ray diffraction, 2 pockets (best druggability 0.45).…

PDB
1PDN
Type
protein + DNA
Length
153 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'- D(*AP*AP*CP*GP*TP*CP*AP*CP*GP*GP*TP*TP*GP*AP*C)-3'); DNA (5'…
UniProt
P06601
Pockets
2 · best druggability 0.45

Structure

x-ray diffraction · 3 distinct chains · 47% helix, 5% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ADNA (5'- D(*AP*AP*CP*GP*TP*CP*AP*CP*GP*GP*TP*TP*GP*AP*C)-3')dna15——
BDNA (5'- D(*TP*TP*GP*TP*CP*AP*AP*CP*CP*GP*TP*GP*AP*CP*G)-3')dna15——
CProtein (prd paired)protein12347% helix, 5% strandP06601

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11250.450.7825empty
21240.390.7517empty

Interfaces

3 interfaces between chains.

  • B–C · 721 Ų buried · 9 hydrogen bonds · protein-nucleic
  • A–C · 720 Ų buried · 14 hydrogen bonds · protein-nucleic
  • A–B · 610 Ų buried · 54 hydrogen bonds · nucleic-nucleic

Compared structures

  • 1PDN · Crystal structure of a paired domain-DNA complex at 2.5 ångströms resolution reveals… · the same entry in another collection · chain A against A, TM-score 1.00
  • P06601 · AlphaFold monomer V2.0 prediction for segmentation protein paired (P06601) · a predicted model of the same protein · chain C against A, TM-score 0.62

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