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MolNFT v1 · #99654 · protein + DNA

ZFP57 mutant (E182Q) in complex with 5-carboxylcytosine DNA

4M9V · DNA (5'-D(*TP*AP*TP*TP*GP*CP*(5CM)P*GP*CP*AP*G)-3'): “ZFP57 mutant (E182Q) in complex with 5-carboxylcytosine DNA”. X-ray diffraction, 2 ligands (ZN, CA), 1 pocket (best druggability 0.59). MolNFT v1 #99654 on GenesisL1: 3D…

PDB
4M9V
Type
protein + DNA
Length
164 residues
Chains
6
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'-D(*TP*AP*TP*TP*GP*CP*(5CM)P*GP*CP*AP*G)-3'); DNA…
UniProt
Q8C6P8
Ligands
ZN, CA
Pockets
1 · best druggability 0.59

Structure

x-ray diffraction · 3 distinct chains · 38% helix, 13% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, DDNA (5'-D(*TP*AP*TP*TP*GP*CP*(5CM)P*GP*CP*AP*G)-3')dna11——
B, EDNA (5'-D(*AP*CP*TP*GP*(1CC)P*GP*GP*CP*AP*AP*T)-3')dna11——
C, FZinc finger protein 57protein6038% helix, 13% strandQ8C6P8

Ligands and binding sites

  • ZN · Zinc ion · metal · 4 copies · chains C, F
  • CA · Calcium ion · metal · 2 copies · chains A, B, D, E
  • MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains B, C, F, E
  • ACT · Acetate ion · additive · 4 copies · chains A, B, C, D, E

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
12390.590.8034MPD

Interfaces

7 interfaces between chains.

  • B–C · 666 Ų buried · 20 hydrogen bonds · protein-nucleic
  • E–F · 656 Ų buried · 19 hydrogen bonds · protein-nucleic
  • A–C · 498 Ų buried · 13 hydrogen bonds · protein-nucleic
  • D–F · 497 Ų buried · 13 hydrogen bonds · protein-nucleic
  • A–B · 462 Ų buried · 30 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 4 modified (nucleotide modification).

Compared structures

  • 4M9V · Zfp57 mutant (E182Q) in complex with 5-carboxylcytosine DNA · the same entry in another collection · chain C against C, TM-score 1.00
  • Q8C6P8 · AlphaFold monomer V2.0 prediction for zinc finger protein 57 (Q8C6P8) · a predicted model of the same protein · chain C against A, TM-score 0.78

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