GL1X · GenesisL1 explorer

MolNFT v1 · #104744 · protein + DNA

Crystal structure of DNA-bound nucleoid associated protein, SAV1473

4QJU · DNA-binding protein hu: “Crystal structure of DNA-bound nucleoid associated protein, SAV1473”. X-ray diffraction, 1 pocket (best druggability 0.78). MolNFT v1 #104744 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
4QJU
Type
protein + DNA
Length
222 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA-binding protein hu; DNA (5'- D(*TP*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP*…
UniProt
Q99U17
Pockets
1 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 30% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, BDNA-binding protein huprotein9042% helix, 30% strandQ99U17
C, DDNA (5'- D(*TP*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP*AP*CP*C)- 3')dna21——

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
19840.780.8072empty

Interfaces

6 interfaces between chains.

  • A–B · 1945 Ų buried · 12 hydrogen bonds · protein-protein
  • C–D · 924 Ų buried · 73 hydrogen bonds · nucleic-nucleic
  • B–D · 577 Ų buried · 10 hydrogen bonds · protein-nucleic
  • B–C · 535 Ų buried · 7 hydrogen bonds · protein-nucleic
  • A–D · 489 Ų buried · 9 hydrogen bonds · protein-nucleic

Compared structures

  • 4QJU · Crystal structure of DNA-bound nucleoid associated protein, SAV1473 · the same entry in another collection · chain A against A, TM-score 1.00
  • Q99U17 · AlphaFold monomer V2.0 prediction for DNA-binding protein hu (Q99U17) · a predicted model of the same protein · chain B against A, TM-score 0.95

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