SMTL ID : 3gl6.1

Crystal structure of JARID1A-PHD3 complexed with H3(1-9)K4me3 peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x ALA- ARG- THR- M3L- GLN- THR- ALA- ARG: Histone H3(Non-covalent)

ALA-ARG-THR-M3L-GLN-THR-ALA-ARG.1: 17 residues within 4Å: Chain A: D.14, K.15, V.16, D.17, W.18, V.19, Q.20, C.21, D.22, D.26, W.28, Q.31, A.41, E.42, E.44, Y.46 Chain B: C.12 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:D.14, A:W.18, A:V.19, A:W.28, A:A.41, A:Y.46 Hydrogen bonds: A:D.14, A:V.16, A:V.16, A:W.18, A:W.18, A:Q.20, A:C.21, A:A.41, A:E.42 Water bridges: A:D.22, A:D.22 Salt bridges: A:D.22, A:D.26 pi-Cation interactions: A:W.18, A:W.18, A:W.28 ALA-ARG-THR-M3L-GLN-THR-ALA-ARG.5: 17 residues within 4Å: Chain A: C.12 Chain B: D.14, K.15, V.16, D.17, W.18, V.19, Q.20, C.21, D.22, D.26, W.28, Q.31, A.41, E.42, E.44, Y.46 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:D.14, B:W.18, B:V.19, B:W.28, B:A.41, B:Y.46 Hydrogen bonds: B:D.14, B:V.16, B:V.16, B:W.18, B:W.18, B:Q.20, B:C.21, B:A.41, B:E.42 Water bridges: B:D.22, B:D.22 Salt bridges: B:D.22, B:D.26 pi-Cation interactions: B:W.18, B:W.18, B:W.28

6 x ZN: ZINC ION(Non-covalent)

ZN.2: 3 residues within 4Å: Chain A: S.1, V.2, C.12 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.1, A:C.12, H2O.18 ZN.3: 4 residues within 4Å: Chain A: C.3, C.8 Chain B: H.30, C.33 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:C.3, A:C.8, B:H.30, B:C.33 ZN.4: 4 residues within 4Å: Chain A: C.21, C.25, C.48, C.51 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.21, A:C.25, A:C.48, A:C.51 ZN.6: 3 residues within 4Å: Chain B: S.1, V.2, C.12 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.1, B:C.12, H2O.50 ZN.7: 4 residues within 4Å: Chain A: H.30, C.33 Chain B: C.3, C.8 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Metal complexes: B:C.3, B:C.8, A:H.30, A:C.33 ZN.8: 4 residues within 4Å: Chain B: C.21, C.25, C.48, C.51 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.21, B:C.25, B:C.48, B:C.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, G.G. et al., Haematopoietic malignancies caused by dysregulation of a chromatin-binding PHD finger. Nature (2009)

Release Date

2009-05-05

Peptides

Histone demethylase JARID1A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Histone demethylase JARID1A

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