SMTL ID : 6h0y.1

Crystal Structure of KDM4D with tetrazolylhydrazide ligand NS022

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.21 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 NA: SODIUM ION(Non-functional Binders)

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

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

EDO.3: 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:K.124, A:K.127, A:N.128 EDO.4: 6 residues within 4Å: Chain A: K.150, Q.151, W.152, N.153, H.156, L.157 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.153, A:N.153 Water bridges: A:N.29, A:W.152, A:W.152 EDO.5: 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.6: 2 residues within 4Å: Chain A: C.168, K.305 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.305, A:K.305 Water bridges: A:C.168 EDO.7: 7 residues within 4Å: Chain A: F.118, E.119, E.122, T.211, R.263, I.264, T.265 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:F.118, A:I.264, A:T.265 Water bridges: A:T.265, A:T.265, A:T.265 EDO.8: 3 residues within 4Å: Chain A: E.27, K.33, Y.37 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.27 EDO.9: 7 residues within 4Å: Chain A: Y.181, E.194, S.200, A.292, I.293, N.294 Ligands: FHZ.14 7 PLIP interactions: 7 interactions with chain A Water bridges: A:Y.181, A:Y.181, A:E.194, A:N.202, A:N.202, A:N.294, A:N.294 EDO.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

SO4.11: 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 SO4.12: 5 residues within 4Å: Chain A: P.113, K.124, N.128, W.185, K.186 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.128 Water bridges: A:N.132 Salt bridges: A:K.186

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

NI.13: 4 residues within 4Å: Chain A: H.192, E.194, H.280 Ligands: FHZ.14 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.192, A:E.194, A:H.280, H2O.5, H2O.8, H2O.12

1 x FHZ: (2~{R})-3-(4-methoxyphenyl)-2-(2~{H}-1,2,3,4-tetrazol-5-yl)propanehydrazide(Non-covalent)

FHZ.14: 14 residues within 4Å: Chain A: Q.88, H.90, Y.136, Y.181, T.188, F.189, A.190, H.192, E.194, K.210, K.245, H.280 Ligands: EDO.9, NI.13 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.136, A:Y.181, A:F.189 Hydrogen bonds: A:Y.136, A:A.190, A:E.194, A:K.210 Water bridges: A:Q.88, A:Y.181 pi-Stacking: A:F.189

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malecki, P.H. et al., Crystal Structure of KDM4D with tetrazolylhydrazide ligand NS022. 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

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