- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.34 Å
- Oligo State
- monomer
- Ligands
- 1 x ZN: ZINC ION(Non-covalent)
ZN.1: 4 residues within 4Å:- Chain A: C.260, H.266, C.332, C.334
4 PLIP interactions:4 interactions with chain A- Metal complexes: A:C.260, A:H.266, A:C.332, A:C.334
- 1 x NI: NICKEL (II) ION(Non-covalent)
NI.2: 4 residues within 4Å:- Chain A: H.214, E.216, H.302
- Ligands: OGA.4
4 PLIP interactions:3 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:H.214, A:E.216, A:H.302, H2O.4
- 1 x MG: MAGNESIUM ION(Non-covalent)
MG.3: 5 residues within 4Å:- Chain A: N.87, I.88, S.89, E.90, I.91
1 PLIP interactions:1 interactions with chain A- Metal complexes: A:N.87
- 1 x OGA: N-OXALYLGLYCINE(Non-covalent)
OGA.4: 12 residues within 4Å:- Chain A: Y.158, F.211, H.214, E.216, S.222, N.224, K.232, W.234, H.302, A.314
- Ligands: NI.2, EDO.12
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:Y.158, A:S.222, A:N.224
- Salt bridges: A:K.232, A:H.302
- 8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.5: 6 residues within 4Å:- Chain A: K.172, Q.173, W.174, N.175, H.178, L.179
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:N.175, A:N.175
- Water bridges: A:N.51, A:W.174, A:W.174
EDO.6: 4 residues within 4Å:- Chain A: P.273, T.274, K.277, R.285
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:P.273, A:R.285, A:R.285
EDO.7: 6 residues within 4Å:- Chain A: E.246, A.262, F.263, L.264, Y.301, S.330
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:L.264, A:Y.301, A:S.330, A:S.330
- Water bridges: A:R.250
EDO.8: 5 residues within 4Å:- Chain A: D.86, N.87, I.88, S.89, E.90
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:S.89
- Water bridges: A:D.86, A:I.88
EDO.9: 6 residues within 4Å:- Chain A: F.140, E.144, T.233, R.285, I.286, T.287
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:I.286, A:T.287
- Water bridges: A:T.287, A:T.287, A:T.287
EDO.10: 6 residues within 4Å:- Chain A: W.79, K.80, A.81, R.82, Y.85, Y.225
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:A.81, A:R.82, A:R.82, A:Y.85, A:Y.225
- Water bridges: A:W.79
EDO.11: 3 residues within 4Å:- Chain A: S.102, T.109, F.253
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:T.109
EDO.12: 6 residues within 4Å:- Chain A: Y.203, E.216, A.314, I.315, N.316
- Ligands: OGA.4
3 PLIP interactions:3 interactions with chain A- Water bridges: A:E.216, A:N.316, A:N.316
- 4 x SO4: SULFATE ION(Non-functional Binders)
SO4.13: 3 residues within 4Å:- Chain A: R.124, H.125, N.128
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:N.128
- Water bridges: A:R.124, A:H.125, A:H.125
- Salt bridges: A:R.124, A:H.125
SO4.14: 4 residues within 4Å:- Chain A: R.82, E.83, T.84, D.86
8 PLIP interactions:8 interactions with chain A- Hydrogen bonds: A:E.83, A:T.84, A:T.84
- Water bridges: A:T.84, A:D.86, A:N.87, A:N.87
- Salt bridges: A:R.82
SO4.15: 3 residues within 4Å:- Chain A: K.146, K.149, N.150
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:N.150
- Water bridges: A:K.149
- Salt bridges: A:K.146, A:K.149
SO4.16: 5 residues within 4Å:- Chain A: P.135, K.146, N.150, W.207, K.208
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:N.150
- Water bridges: A:K.208
- Salt bridges: A:K.208
- 1 x 71N: 2-(trifluoromethyl)-1H-benzimidazol-5-amine(Covalent)
71N.17: 7 residues within 4Å:- Chain A: E.61, H.66, Y.221, F.297, P.298, R.321, Y.325
4 PLIP interactions:4 interactions with chain A- Water bridges: A:E.61, A:R.321
- pi-Stacking: A:H.66
- Halogen bonds: A:E.61
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Pearce, N.M. et al., A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density. Nat Commun (2017)
- Release Date
- 2017-03-15
- Peptides
- Lysine-specific demethylase 4D: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A
SMTL ID : 5ph0.1
PanDDA analysis group deposition -- Crystal Structure of JMJD2D in complex with N09484a
Lysine-specific demethylase 4D
Related Entries With Identical Sequence
5ph1.1 | 5ph2.1 | 5ph3.1 | 5ph4.1 | 5ph5.1 | 5ph6.1 | 5ph7.1 | 5ph8.1 | 5ph9.1 | 5pha.1 | 5phb.1 | 5phc.1 | 5phd.1 | 5phe.1 | 5phf.1 | 5phg.1 | 5phh.1 | 5phi.1 | 5phj.1 | 5phk.1 | 5phl.1 | 5phm.1 | 5phn.1 | 5pho.1 | 5php.1 | 5phq.1 | 5phr.1 | 5phs.1 | 5pht.1 | 5phu.1 more...less...5phv.1 | 5phw.1 | 5phx.1 | 5phy.1 | 5phz.1 | 5pi0.1 | 5pi1.1 | 5pi2.1 | 5pi3.1 | 5pi4.1 | 5pi5.1 | 5pi6.1 | 5pi7.1 | 5pi8.1 | 5pi9.1 | 5pia.1 | 5pib.1 | 5pic.1 | 5pid.1 | 5pie.1 | 5pif.1 | 5pig.1 | 5pih.1 | 5pii.1 | 5pij.1 | 5pik.1 | 5pil.1 | 5pim.1 | 5pin.1 | 5pio.1 | 5pip.1 | 5piq.1 | 5pir.1 | 5pis.1 | 5pit.1 | 5piu.1 | 5piv.1 | 5piw.1 | 5pix.1 | 5piy.1 | 5piz.1 | 5pj0.1 | 5pj1.1 | 5pj2.1 | 5pj3.1 | 5pj4.1 | 5pj5.1 | 5pj6.1 | 5pj7.1 | 5pj8.1 | 5pj9.1 | 5pja.1 | 5pjb.1 | 5pjc.1 | 5pjd.1 | 5pje.1 | 5pjf.1 | 5pjg.1 | 5pjh.1 | 5pji.1 | 5pjj.1 | 5pjk.1 | 5pjl.1 | 5pjm.1 | 5pjn.1 | 5pjo.1 | 5pjp.1 | 5pjq.1 | 5pjr.1 | 5pjs.1 | 5pjt.1 | 5pju.1 | 5pjv.1 | 5pjw.1 | 5pjx.1 | 5pjy.1 | 5pjz.1 | 5pk0.1 | 5pk1.1 | 5pk2.1 | 5pk3.1 | 5pk4.1 | 5pk5.1 | 5pk6.1 | 5pk7.1 | 5pk8.1 | 5pk9.1 | 5pka.1 | 5pkb.1 | 5pkc.1 | 5pkd.1 | 5pke.1 | 5pkf.1 | 5pkg.1 | 5pkh.1 | 5pki.1 | 5pkj.1 | 5pkk.1 | 5pkl.1 | 5pkm.1 | 5pkn.1 | 5pko.1 | 5pkp.1 | 5pkq.1 | 5pkr.1 | 5pks.1 | 5pkt.1 | 5pku.1 | 5pkv.1 | 5pkw.1 | 5pkx.1 | 5pky.1 | 5pkz.1 | 5pl0.1 | 5pl1.1 | 5pl2.1 | 5pl3.1 | 5pl4.1 | 5pl5.1 | 5pl6.1 | 5pl7.1 | 5pl8.1 | 5pl9.1 | 5pla.1 | 5plb.1 | 5plc.1 | 5pld.1 | 5ple.1 | 5plf.1 | 5plg.1 | 5plh.1 | 5pli.1 | 5plj.1 | 5plk.1 | 5pll.1 | 5plm.1 | 5pln.1 | 5plo.1 | 5plp.1 | 5plq.1 | 5plr.1 | 5pls.1 | 5plt.1 | 5plu.1 | 5plv.1 | 5plw.1 | 5plx.1 | 5ply.1 | 5plz.1 | 5pm0.1 | 5pm1.1 | 5pm2.1 | 5pm3.1 | 5pm4.1 | 5pm5.1 | 5pm6.1 | 5pm7.1 | 5pm8.1 | 5pm9.1 | 5pma.1 | 5pmb.1 | 5pmc.1 | 5pmd.1 | 5pme.1 | 5pmf.1 | 5pmg.1 | 5pmh.1 | 5pmi.1 | 5pmj.1 | 5pmk.1 | 5pml.1 | 5pmm.1 | 5pmn.1 | 5pmo.1 | 5pmp.1 | 5pmq.1 | 5pmr.1 | 5pms.1 | 5pmt.1 | 5pmu.1 | 5pmv.1 | 5pmw.1 | 5pmx.1 | 5pmy.1 | 5pmz.1 | 5pn0.1 | 5pn1.1 | 5pn2.1 | 5pn3.1 | 5pn4.1 | 5pn5.1 | 5pn6.1 | 5pn7.1 | 5pn8.1 | 5pn9.1 | 5pna.1 | 5pnb.1 | 5pnc.1 | 5pnd.1 | 5pne.1 | 5pnf.1 | 5png.1 | 5pnh.1 | 5pni.1 | 5pnj.1 | 5pnk.1 | 5pnl.1 | 5pnm.1 | 5pnn.1 | 5pno.1 | 5pnp.1 | 5pnq.1 | 5pnr.1 | 5pns.1 | 5pnu.1 | 5pnv.1 | 5pnw.1