SMTL ID : 8f8z.2 (1 other biounit)

PHF2 (PHD+JMJ) in Complex with H3 Histone N-Terminal Peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 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

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 2 residues within 4Å: Chain A: A.6, T.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.7 EDO.10: 2 residues within 4Å: Chain A: C.174, K.175 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.175

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

SO4.4: 4 residues within 4Å: Chain A: T.21, R.22, F.23, S.37 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.23, A:S.37, A:S.37, A:S.37 Salt bridges: A:R.22 SO4.5: 5 residues within 4Å: Chain A: K.136, D.137, G.138, L.139, G.140 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.138, A:G.140, A:L.141 Salt bridges: A:K.136 SO4.6: 2 residues within 4Å: Chain A: A.233, K.234 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.234 SO4.7: 3 residues within 4Å: Chain A: P.396, P.397, H.398 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.398 Salt bridges: A:H.398 SO4.8: 2 residues within 4Å: Chain A: A.278, S.279 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.279 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 SO4.11: 5 residues within 4Å: Chain A: Y.184, N.189, R.190, K.191, R.192 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.187, A:N.189, A:K.191, A:R.192 Salt bridges: A:R.192 SO4.12: 3 residues within 4Å: Chain A: R.276, K.305, Y.307 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.304, A:K.305, A:Y.307 Salt bridges: A:R.276 SO4.13: 4 residues within 4Å: Chain A: Y.225, S.343, H.380, L.399 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.343, A:S.343 Salt bridges: A:H.380 SO4.14: 6 residues within 4Å: Chain A: Y.149, V.150, Y.185, Y.186, K.267 Chain B: K.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.150, A:Y.185, A:Y.185 Salt bridges: A:K.267

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
H3 N-Terminal Peptide: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
F

Lysine-specific demethylase PHF2

H3 N-Terminal Peptide

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