SMTL ID : 6h0z.1

Crystal Structure of KDM4D with tetrazolylhydrazide ligand NR067

Coordinates

PDB Format Compare

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.238, H.244, C.310, C.312 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.238, A:H.244, A:C.310, A:C.312

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

CL.2: 3 residues within 4Å: Chain A: N.128, W.185, K.186 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 3 residues within 4Å: Chain A: N.17, F.261, N.262 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.261, A:N.262

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

EDO.4: 4 residues within 4Å: Chain A: R.123, K.124, K.127, N.128 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.123, A:R.123, A:R.123, A:K.124, A:N.128 EDO.5: 6 residues within 4Å: Chain A: K.150, Q.151, W.152, N.153, H.156, L.157 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.153, A:N.153 Water bridges: A:N.29, A:W.152, A:W.152, A:N.153 EDO.6: 4 residues within 4Å: Chain A: P.251, T.252, K.255, R.263 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.251, A:R.263, A:R.263 EDO.7: 7 residues within 4Å: Chain A: Y.179, Y.181, E.194, S.200, I.293, N.294 Ligands: FHQ.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.200, A:S.200, A:N.294

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

SO4.8: 4 residues within 4Å: Chain A: R.60, E.61, T.62, N.65 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:E.61, A:T.62, A:T.62, A:N.65 Water bridges: A:R.60, A:R.60, A:R.60, A:T.62 Salt bridges: A:R.60 SO4.9: 1 residues within 4Å: Chain A: K.255 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.255

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

NI.10: 4 residues within 4Å: Chain A: H.192, E.194, H.280 Ligands: FHQ.12 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.192, A:E.194, A:H.280, H2O.9

2 x FHQ: ~{N}-[(~{E})-(4-bromophenyl)methylideneamino]-2-(2~{H}-1,2,3,4-tetrazol-5-yl)ethanamide(Non-covalent)

FHQ.11: 10 residues within 4Å: Chain A: Y.63, A.105, N.106, Q.111, T.112, L.206, G.207, E.208, G.286, F.287 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.206, A:E.208, A:F.287, A:F.287 Hydrogen bonds: A:A.105, A:N.106, A:T.112, A:E.208, A:F.287 Water bridges: A:T.112, A:T.112 Halogen bonds: A:Y.63 FHQ.12: 12 residues within 4Å: Chain A: Y.136, Y.181, F.189, H.192, E.194, S.200, N.202, K.210, W.212, H.280 Ligands: EDO.7, NI.10 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.189, A:W.212 Hydrogen bonds: A:Y.136, A:S.200, A:S.200, A:K.210 Water bridges: A:T.188, A:N.202

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malecki, P.H. et al., Crystal Structure of KDM4D with tetrazolylhydrazide ligand NR067. To be published

Release Date

2020-01-29

Peptides

Lysine-specific demethylase 4D: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysine-specific demethylase 4D

Related Entries With Identical Sequence