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MolNFT v1 · #36230 · protein + DNA

Solution structure of a complex of the second DNA binding domain of human hmg-I(Y) bound to DNA dodecamer containing the prdii site of the interferon-beta promoter, NMR, 35 structures

2EZE · DNA (5'-D(*GP*GP*GP*AP*AP*AP*TP*TP*CP*CP*TP*C)-3'): “Solution structure of a complex of the second DNA binding domain of human hmg-I(Y) bound to DNA dodecamer…”. Solution nmr, 1 pocket (best druggability 0.29). MolNFT v1 #36230 on…

PDB
2EZE
Type
protein + DNA
Length
49 residues
Chains
3
Method
solution nmr
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'-D(*GP*GP*GP*AP*AP*AP*TP*TP*CP*CP*TP*C)-3'); DNA…
UniProt
P17096
Pockets
1 · best druggability 0.29

Structure

solution nmr · 3 distinct chains · 0% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
BDNA (5'-D(*GP*GP*GP*AP*AP*AP*TP*TP*CP*CP*TP*C)-3')dna12——
CDNA (5'-D(*GP*AP*GP*GP*AP*AP*TP*TP*TP*CP*CP*C)-3')dna12——
AHigh mobility group protein hmg-I/HMG-Yprotein250% helix, 0% strandP17096

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1630.290.7510empty

Interfaces

3 interfaces between chains.

  • B–C · 553 Ų buried · 42 hydrogen bonds · nucleic-nucleic
  • B–A · 498 Ų buried · 8 hydrogen bonds · protein-nucleic
  • C–A · 363 Ų buried · 10 hydrogen bonds · protein-nucleic

Compared structures

  • 2EZE · Solution structure of a complex of the second DNA binding domain of human hmg-I(Y) bound… · the same entry in another collection · chain B against B, TM-score 1.00
  • P17096 · AlphaFold monomer V2.0 prediction for high mobility group protein hmg-I/HMG-Y (P17096) · a predicted model of the same protein · chain A against A, TM-score 0.19

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