SMTL ID : 5ly1.1

JMJD2A/ KDM4A COMPLEXED WITH NI(II) AND Macrocyclic PEPTIDE Inhibitor CP2 (13-mer)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-4-1-mer

Ligands

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

NI.1: 3 residues within 4Å: Chain A: H.210, E.212, H.298 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.210, A:E.212, A:H.298, H2O.3, H2O.3 NI.6: 3 residues within 4Å: Chain B: H.210, E.212, H.298 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.210, B:E.212, B:H.298, H2O.5 NI.12: 3 residues within 4Å: Chain C: H.210, E.212, H.298 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.210, C:E.212, C:H.298, H2O.7, H2O.9 NI.16: 3 residues within 4Å: Chain D: H.210, E.212, H.298 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.210, D:E.212, D:H.298, H2O.15, H2O.15

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.7: 4 residues within 4Å: Chain B: C.256, H.262, C.328, 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.13: 4 residues within 4Å: Chain C: C.256, H.262, C.328, 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.17: 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

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

CL.3: 5 residues within 4Å: Chain A: F.249, P.250, G.251, S.252 Chain B: K.127 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain C: F.249, P.250, G.251, S.252 Chain D: K.127 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain D: F.249, P.250, G.251, S.252 Ligand excluded by PLIP

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: E.45, Y.55, F.375 No protein-ligand interaction detected (PLIP) GOL.8: 4 residues within 4Å: Chain B: E.45, Y.52, Y.55, F.375 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.45, B:E.45 GOL.9: 9 residues within 4Å: Chain B: R.47, N.48, F.49, D.168, E.169, W.170, N.171, R.174, L.175 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.47, B:N.48, B:F.49, B:W.170, B:N.171, B:N.171 GOL.11: 4 residues within 4Å: Chain C: E.45, Y.52, Y.55, F.375 2 PLIP interactions: 2 interactions with chain C Water bridges: C:E.44, C:E.45 GOL.15: 8 residues within 4Å: Chain C: D.215, K.239, Y.295, Y.321, Q.324, A.325, I.363, H.365 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.215, C:K.239, C:Y.321 Water bridges: C:V.326

3 x PPI: PROPANOIC ACID(Non-covalent)

PPI.5: 8 residues within 4Å: Chain A: G.192, Y.197, Y.199, E.212, S.218, S.310, T.311, N.312 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.197 Hydrogen bonds: A:Y.199, A:N.312 PPI.10: 6 residues within 4Å: Chain B: G.192, Y.197, Y.199, E.212, S.310, T.311 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.197 Hydrogen bonds: B:S.310, B:N.312 Water bridges: B:N.220 PPI.19: 8 residues within 4Å: Chain D: G.192, Y.197, Y.199, E.212, S.218, S.310, T.311, N.312 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:Y.197 Hydrogen bonds: D:Y.199, D:E.212, D:N.312

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: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Lysine-specific demethylase 4A

CP2

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