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MolNFT v1 · #158091 · protein + DNA

Structure of tbp-hoogsteen containing DNA complex

6NJQ · Tata-box-binding protein 1: “Structure of tbp-hoogsteen containing DNA complex”. X-ray diffraction, 3 pockets (best druggability 0.39). MolNFT v1 #158091 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
6NJQ
Type
protein + DNA
Length
430 residues
Chains
6
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Tata-box-binding protein 1; DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*CP*GP*GP*GP*CP*A)-3'); DNA…
UniProt
P28147
Pockets
3 · best druggability 0.39

Structure

x-ray diffraction · 3 distinct chains · 26% helix, 35% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
B, ATata-box-binding protein 1protein18726% helix, 35% strandP28147
E, CDNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*CP*GP*GP*GP*CP*A)-3')dna14——
F, DDNA (5'-D(*TP*GP*CP*CP*CP*GP*TP*TP*TP*AP*TP*AP*GP*C)-3')dna14——

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11650.390.7216empty
21480.370.7318empty
3560.310.7615empty

Interfaces

7 interfaces between chains.

  • A–D · 826 Ų buried · 9 hydrogen bonds · protein-nucleic
  • B–E · 819 Ų buried · 9 hydrogen bonds · protein-nucleic
  • B–F · 816 Ų buried · 9 hydrogen bonds · protein-nucleic
  • A–C · 792 Ų buried · 5 hydrogen bonds · protein-nucleic
  • C–D · 623 Ų buried · 62 hydrogen bonds · nucleic-nucleic

Compared structures

  • 6NJQ · Structure of TBP-Hoogsteen containing DNA complex · the same entry in another collection · chain F against F, TM-score 1.00
  • P28147 · AlphaFold monomer V2.0 prediction for tata-box-binding protein 1 (P28147) · a predicted model of the same protein · chain B against A, TM-score 0.99

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