SMTL ID : 6i9m.1

JmjC domain-containing protein 5 (JMJD5) in complex with Mn and R-2-hydroxyglutarate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 5 residues within 4Å: Chain A: H.161, D.163, H.240, W.254 Ligands: 2HG.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.161, A:D.163, A:H.240, H2O.3

1 x 2HG: (2R)-2-hydroxypentanedioic acid(Non-covalent)

2HG.2: 14 residues within 4Å: Chain A: Y.112, W.150, S.158, H.161, D.163, N.167, L.169, K.176, H.240, V.242, S.252, W.254 Ligands: MN.1, GOL.5 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.150, A:W.150, A:V.242 Hydrogen bonds: A:Y.112, A:S.158, A:N.167, A:W.254 Water bridges: A:S.158 Salt bridges: A:K.176, A:H.240

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.3: 7 residues within 4Å: Chain A: L.40, V.41, P.42, G.43, Q.166, P.235, V.236 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.166 Water bridges: A:V.236, A:V.236

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: R.29, P.30, S.31, L.32, V.51, D.133, Y.134 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.29, A:L.32, A:D.133 Water bridges: A:R.29, A:V.51 GOL.5: 8 residues within 4Å: Chain A: Q.115, W.150, S.158, P.159, H.161, N.199, T.200 Ligands: 2HG.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.115, A:S.158, A:N.199 Water bridges: A:Q.115 GOL.6: 7 residues within 4Å: Chain A: P.159, H.192, T.200, S.201, Q.202, V.203, D.204 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.192, A:Q.202 Water bridges: A:L.160

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Islam, M.S. et al., Structural analysis of the 2-oxoglutarate binding site of the circadian rhythm linked oxygenase JMJD5. Sci Rep (2022)

Release Date

2019-12-04

Peptides

JmjC domain-containing protein 5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

JmjC domain-containing protein 5

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