SMTL ID : 6f5t.1

Crystal Structure of KDM4D with tetrazole ligand GF057

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.228, H.234, C.300, C.302 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.228, A:H.234, A:C.300, A:C.302

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

SO4.2: 3 residues within 4Å: Chain A: R.92, H.93, N.96 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.96 Water bridges: A:H.93, A:H.93, A:H.93 Salt bridges: A:R.92, A:H.93 SO4.3: 5 residues within 4Å: Chain A: D.54, N.55, I.56, S.57, R.92 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.55, A:S.57, A:S.57, A:S.57 Salt bridges: A:R.92 SO4.4: 5 residues within 4Å: Chain A: P.103, K.114, N.118, W.175, K.176 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.118, A:W.175 Water bridges: A:N.122 Salt bridges: A:K.176 SO4.5: 4 residues within 4Å: Chain A: R.113, K.114, K.117, N.118 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.118 Salt bridges: A:R.113, A:K.114, A:K.117

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

NI.6: 4 residues within 4Å: Chain A: H.182, E.184, H.270 Ligands: CQK.7 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.182, A:E.184, A:H.270, H2O.2

1 x CQK: ~{N}-oxidanyl-4-(2~{H}-1,2,3,4-tetrazol-5-yl)pyridine-2-carboxamide(Non-covalent)

CQK.7: 10 residues within 4Å: Chain A: Y.126, Y.171, F.179, H.182, E.184, K.200, W.202, K.235, H.270 Ligands: NI.6 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.171, A:F.179, A:W.202 Hydrogen bonds: A:Y.171, A:K.235, A:K.235 Water bridges: A:Y.169, A:K.200, A:K.200, A:N.274, A:N.274, A:N.284, A:N.284 pi-Stacking: A:Y.171, A:F.179

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.8: 7 residues within 4Å: Chain A: M.9, F.11, H.12, Y.24, Y.27, Q.31 Ligands: EPE.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.12, A:Y.24 Water bridges: A:I.10, A:H.12 EPE.9: 5 residues within 4Å: Chain A: E.17, K.23, Y.24, Y.27 Ligands: EPE.8 5 PLIP interactions: 5 interactions with chain A Water bridges: A:E.17, A:Y.27 Salt bridges: A:E.17, A:E.17, A:K.23

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

EDO.10: 2 residues within 4Å: Chain A: Y.293, M.296 No protein-ligand interaction detected (PLIP) EDO.11: 3 residues within 4Å: Chain A: F.108, I.254, T.255 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.255, A:T.255 Water bridges: A:K.40, A:T.201, A:T.255 EDO.12: 6 residues within 4Å: Chain A: F.18, N.19, D.20, F.21, Q.141, W.142 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.18, A:F.21, A:W.142 Water bridges: A:D.20, A:D.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malecki, P.H. et al., Crystal Structure of KDM4D with tetrazole 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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