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MolNFT v1 · #24427 · protein + DNA

The nuclease domain of adeno-associated virus rep complexed with the rbe' stemloop of the viral inverted terminal repeat

1UUT · Rep protein: “The nuclease domain of adeno-associated virus rep complexed with the rbe' stemloop of the viral inverted…”. X-ray diffraction, 2 ligands (MG, CL), 3 pockets (best druggability 0.31). MolNFT v1 #24427 on GenesisL1: 3D…

PDB
1UUT
Type
protein + DNA
Length
420 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Rep protein; 5'-D(*CP*AP*GP*CP*TP*CP*TP*TP*TP*GP *AP*GP*CP*TP*G)-3'
UniProt
Q9YJC1
Ligands
MG, CL
Pockets
3 · best druggability 0.31

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 17% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, BRep proteinprotein19543% helix, 17% strandQ9YJC1
C, D5'-D(*CP*AP*GP*CP*TP*CP*TP*TP*TP*GP *AP*GP*CP*TP*G)-3'dna15——

Ligands and binding sites

  • MG · Magnesium ion · metal · 4 copies · chains A, B, C
  • CL · Chloride ion · ion · chains A

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1800.310.7311empty
2580.290.7414empty
3560.290.7511empty

Interfaces

3 interfaces between chains.

  • A–B · 438 Ų buried · 3 hydrogen bonds · protein-protein
  • B–D · 371 Ų buried · 10 hydrogen bonds · protein-nucleic
  • A–C · 366 Ų buried · 11 hydrogen bonds · protein-nucleic

Compared structures

  • 1UUT · The Nuclease Domain of Adeno-Associated Virus Rep Complexed with the RBE' Stemloop of the… · the same entry in another collection · chain A against A, TM-score 1.00

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