SMTL ID : 7m10.1

PHF2 PHD Domain Complexed with Peptide From N-terminus of VRK1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.15 Å

Oligo State

hetero-1-1-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.27, C.30, C.54, C.57 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.27, A:C.30, A:C.54, A:C.57 ZN.2: 4 residues within 4Å: Chain A: C.12, C.14, H.35, C.38 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.12, A:C.14, A:H.35, A:C.38

6 x FMT: FORMIC ACID(Non-functional Binders)

FMT.3: 5 residues within 4Å: Chain A: V.10, Y.11, C.12, D.32, W.33 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:C.12, A:W.33 Water bridges: A:R.15, A:D.32 FMT.4: 2 residues within 4Å: Chain A: C.30, K.31 No protein-ligand interaction detected (PLIP) FMT.5: 3 residues within 4Å: Chain A: A.46, P.47 Chain B: V.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.46 FMT.6: 5 residues within 4Å: Chain A: G.36, S.37, G.40, V.41, E.42 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.43 FMT.7: 1 residues within 4Å: Chain A: K.59 No protein-ligand interaction detected (PLIP) FMT.8: 3 residues within 4Å: Chain A: W.33 Chain B: R.2, K.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.2 Water bridges: B:V.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, J. et al., Histone H3 N-terminal mimicry drives a novel network of methyl-effector interactions. Biochem.J. (2021)

Release Date

2021-05-26

Peptides

Lysine-specific demethylase PHF2: A
Serine/threonine-protein kinase VRK1 N-terminus peptide: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lysine-specific demethylase PHF2

Serine/threonine-protein kinase VRK1 N-terminus peptide

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