SMTL ID : 5ly2.1

JMJD2A/ KDM4A COMPLEXED WITH NI(II), NOG AND Macrocyclic PEPTIDE Inhibitor CP2_R6Kme3 (13-mer)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.43 Å

Oligo State

hetero-4-4-mer

Ligands

4 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 4 residues within 4Å: Chain A: H.210, E.212, H.298 Ligands: OGA.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.210, A:E.212, A:H.298, H2O.3 NI.7: 4 residues within 4Å: Chain B: H.210, E.212, H.298 Ligands: OGA.10 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.210, B:E.212, B:H.298, H2O.7 NI.14: 4 residues within 4Å: Chain C: H.210, E.212, H.298 Ligands: OGA.17 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.210, C:E.212, C:H.298, H2O.12 NI.19: 4 residues within 4Å: Chain D: H.210, E.212, H.298 Ligands: OGA.22 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.210, D:E.212, D:H.298, H2O.16

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.256, H.262, C.328, C.330 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.256, A:H.262, A:C.328, A:C.330 ZN.8: 5 residues within 4Å: Chain B: C.256, H.262, C.328, S.329, C.330 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.256, B:H.262, B:C.328, B:C.330 ZN.15: 5 residues within 4Å: Chain C: C.256, H.262, C.328, S.329, C.330 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.256, C:H.262, C:C.328, C:C.330 ZN.20: 4 residues within 4Å: Chain D: C.256, H.262, C.328, C.330 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.256, D:H.262, D:C.328, D:C.330

4 x OGA: N-OXALYLGLYCINE(Non-covalent)

OGA.3: 14 residues within 4Å: Chain A: Y.154, Y.199, F.207, H.210, E.212, S.218, N.220, K.228, W.230, T.292, H.298, S.310 Chain E: K.7 Ligands: NI.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.218, A:N.220, A:S.310 Salt bridges: A:K.228, A:H.298 OGA.10: 14 residues within 4Å: Chain B: Y.154, Y.199, F.207, H.210, E.212, S.218, N.220, K.228, W.230, T.292, H.298, S.310 Chain F: K.7 Ligands: NI.7 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.154, B:S.218, B:N.220, B:S.310, B:S.310 Salt bridges: B:K.228, B:H.298 OGA.17: 12 residues within 4Å: Chain C: Y.154, F.207, H.210, E.212, S.218, N.220, K.228, W.230, T.292, H.298, S.310 Ligands: NI.14 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Y.154, C:S.218, C:N.220, C:S.310 Salt bridges: C:K.228, C:H.298 OGA.22: 12 residues within 4Å: Chain D: Y.154, Y.199, F.207, H.210, E.212, S.218, N.220, K.228, W.230, H.298, S.310 Ligands: NI.19 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.218, D:N.220, D:S.310 Water bridges: D:E.212 Salt bridges: D:K.228

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 2 residues within 4Å: Chain A: D.333 Chain E: Y.4 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:D.333, A:D.333, E:N.5 GOL.5: 3 residues within 4Å: Chain A: Y.81, D.82, D.85 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.81 GOL.11: 3 residues within 4Å: Chain B: G.160, T.161, L.162 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.161 Water bridges: B:R.78 GOL.12: 8 residues within 4Å: Chain B: D.213, R.261, H.262, C.328, M.334, V.335 Chain F: N.5, W.10 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:R.261, B:V.335, F:W.10 GOL.13: 4 residues within 4Å: Chain B: Y.107, N.108, M.264 Chain F: W.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.108, B:N.108

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 4 residues within 4Å: Chain A: F.249, G.251, S.252 Chain B: K.127 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: K.127 Chain B: F.249, G.251, S.252 Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain C: Y.81 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain C: F.249, G.251 Chain D: K.127 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain D: F.249, P.250, G.251, S.252 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kawamura, A. et al., Highly selective inhibition of histone demethylases by de novo macrocyclic peptides. Nat Commun (2017)

Release Date

2017-04-12

Peptides

Lysine-specific demethylase 4A: ABCD
CP2_R6Kme3: EFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Lysine-specific demethylase 4A

CP2_R6Kme3

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