SMTL ID : 8f8y.1 (1 other biounit)

PHF2 (PHD+JMJ) in Complex with VRK1 N-Terminal Peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.06 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

10 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 2 residues within 4Å: Chain A: R.22, S.37 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.37 Salt bridges: A:R.22 SO4.4: 6 residues within 4Å: Chain A: Y.149, V.150, Y.185, Y.186, K.267 Chain B: K.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.150 Salt bridges: A:K.267 SO4.5: 5 residues within 4Å: Chain A: K.136, D.137, G.138, L.139, G.140 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.136, A:G.138, A:L.139, A:G.140 Salt bridges: A:K.136 SO4.6: 2 residues within 4Å: Chain A: P.397, H.398 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.398 Salt bridges: A:H.398 SO4.7: 3 residues within 4Å: Chain A: Y.184, K.191, R.192 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.187, A:K.191, A:R.192 Salt bridges: A:R.192 SO4.8: 3 residues within 4Å: Chain A: R.289, H.294, G.362 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.362 Salt bridges: A:R.289, A:H.294 SO4.9: 3 residues within 4Å: Chain A: R.111, K.312, Q.315 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.315 Salt bridges: A:R.111, A:K.312 SO4.10: 1 residues within 4Å: Chain A: R.205 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.205 SO4.11: 2 residues within 4Å: Chain A: R.111, P.134 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.111 SO4.12: 3 residues within 4Å: Chain A: P.47, K.68, S.187 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.187 Salt bridges: A:K.68

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Horton, J.R. et al., A complete methyl-lysine binding aromatic cage constructed by two domains of PHF2. J.Biol.Chem. (2022)

Release Date

2023-01-18

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
E

Lysine-specific demethylase PHF2

Serine/threonine-protein kinase VRK1 N-terminus peptide

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