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MolNFT v1 · #181646 · protein

PHF2 phd domain complexed with peptide from N-terminus of VRK1

7M10 · Lysine-specific demethylase PHF2: “PHF2 phd domain complexed with peptide from N-terminus of VRK1”. X-ray diffraction, 1 ligand (ZN). MolNFT v1 #181646 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
7M10
Type
protein
Length
76 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Lysine-specific demethylase PHF2; SERINE/THREONINE-protein kinase VRK1 N-terminus peptide
EC
1.14.11.-, 2.7.11.1
UniProt
O75151, Q99986
Ligands
ZN

Structure

x-ray diffraction · 2 distinct chains · 20% helix, 22% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ALysine-specific demethylase PHF2 (EC 1.14.11.-)protein6822% helix, 22% strandO75151
BSERINE/THREONINE-protein kinase VRK1 N-terminus peptide (EC 2.7.11.1)protein80% helix, 25% strandQ99986

Ligands and binding sites

  • ZN · Zinc ion · metal · 2 copies · chains A
  • FMT · Formic acid · additive · 6 copies · chains A, B

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

Interfaces

1 interface between chains.

  • A–B · 597 Ų buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 modified (methylation).

Compared structures

  • 7M10 · PHF2 PHD Domain Complexed with Peptide From N-terminus of VRK1 · the same entry in another collection · chain A against A, TM-score 1.00
  • O75151 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase PHF2 (O75151) · a predicted model of the same protein · chain A against A, TM-score 0.89

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