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MolNFT v1 · #11374 · protein + DNA

Testing the water-mediated hin recombinase DNA recognition by systematic mutations

1JKR · 5'-D(*TP*GP*TP*TP*TP*TP*TP*GP*AP*CP*AP*AP*GP*A)- 3': “Testing the water-mediated hin recombinase DNA recognition by systematic mutations”. X-ray diffraction, 1 pocket (best druggability 0.31). MolNFT v1 #11374 on GenesisL1: 3D…

PDB
1JKR
Type
protein + DNA
Length
74 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'-D(*TP*GP*TP*TP*TP*TP*TP*GP*AP*CP*AP*AP*GP*A)- 3'…
UniProt
P03013
Pockets
1 · best druggability 0.31

Structure

x-ray diffraction · 3 distinct chains · 54% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A5'-D(*TP*GP*TP*TP*TP*TP*TP*GP*AP*CP*AP*AP*GP*A)- 3'dna14——
B5'-D(*AP*TP*CP*TP*TP*GP*TP*CP*AP*AP*AP*AP*AP*C)- 3'dna14——
CDNA-invertase hinprotein4654% helix, 0% strandP03013

Ligands and binding sites

  • TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1620.310.7512empty

Interfaces

3 interfaces between chains.

  • A–B · 526 Ų buried · 52 hydrogen bonds · nucleic-nucleic
  • A–C · 457 Ų buried · 12 hydrogen bonds · protein-nucleic
  • B–C · 407 Ų buried · 5 hydrogen bonds · protein-nucleic

Compared structures

  • 1JKR · Testing the Water-Mediated HIN Recombinase DNA Recognition by Systematic Mutations · the same entry in another collection · chain A against A, TM-score 1.00
  • P03013 · AlphaFold monomer V2.0 prediction for DNA-invertase hin (P03013) · a predicted model of the same protein · chain C against A, TM-score 0.93

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