SMTL ID : 6f5q.1

Crystal Structure of KDM4D with GF026 ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.43 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: 4 residues within 4Å: Chain A: P.113, N.128, W.185, K.186 Ligand excluded by PLIP

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

EDO.3: 4 residues within 4Å: Chain A: R.123, K.124, K.127, N.128 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.123, A:R.123, A:R.123, 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, R.263 Ligands: EDO.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.251, A:R.263, A:R.263 EDO.6: 5 residues within 4Å: Chain A: K.109, Q.111, N.132, W.185, K.186 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.111, A:N.132 Water bridges: A:Q.111 EDO.7: 5 residues within 4Å: Chain A: E.122, R.123, W.126, P.251 Ligands: EDO.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.122 Water bridges: A:R.123 EDO.8: 6 residues within 4Å: Chain A: F.118, E.122, T.211, R.263, I.264, T.265 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.265 Water bridges: A:T.265 EDO.9: 3 residues within 4Å: Chain A: E.27, Y.34, Y.37 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.27 EDO.10: 3 residues within 4Å: Chain A: T.24, K.25, E.26 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.25, A:K.25, A:E.26 EDO.11: 7 residues within 4Å: Chain A: Y.181, E.194, S.200, A.292, I.293, N.294 Ligands: CTK.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.181, A:I.293 Water bridges: A:S.200

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

SO4.12: 4 residues within 4Å: Chain A: R.60, E.61, T.62, N.65 11 PLIP interactions: 11 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:R.60, A:R.60, A:T.62 Salt bridges: A:R.60 SO4.13: 3 residues within 4Å: Chain A: R.102, H.103, N.106 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.106 Water bridges: A:H.103, A:H.103 Salt bridges: A:H.103

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

NI.14: 4 residues within 4Å: Chain A: H.192, E.194, H.280 Ligands: CTK.15 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.192, A:E.194, A:H.280, H2O.2, H2O.6

1 x CTK: 2-[2-(methylsulfonylamino)ethylamino]pyridine-4-carboxylic acid(Non-covalent)

CTK.15: 13 residues within 4Å: Chain A: H.90, Y.136, Y.181, T.188, F.189, A.190, H.192, K.210, W.212, K.245, H.280 Ligands: EDO.11, NI.14 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.189, A:W.212 Hydrogen bonds: A:Q.88, A:Y.136, A:A.190 Water bridges: A:N.202 Salt bridges: A:K.210 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 GF026 ligand. To be published

Release Date

2018-12-12

Peptides

Lysine-specific demethylase 4D: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysine-specific demethylase 4D

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