SMTL ID : 7yxh.1

Drosophila melanogaster JMJD7 (dmJMJD7) in complex with Mn and succinate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: H.181, D.183, H.284, W.298 Ligands: SIN.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.181, A:D.183, A:H.284, H2O.3 MN.5: 4 residues within 4Å: Chain B: H.181, D.183, Y.185, H.284 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.181, B:D.183, B:H.284, H2O.5, H2O.5

1 x SIN: SUCCINIC ACID(Non-covalent)

SIN.2: 13 residues within 4Å: Chain A: Y.129, W.170, T.178, H.181, D.183, N.187, Y.189, K.196, F.198, H.284, V.286, W.298 Ligands: MN.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.170, A:Y.189 Hydrogen bonds: A:Y.129, A:T.178, A:N.187, A:Y.189 Water bridges: A:K.196, A:W.298 Salt bridges: A:H.181, A:K.196, A:H.284

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

EDO.3: 5 residues within 4Å: Chain A: N.161, K.162, D.302 Chain B: E.45, K.49 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.161, A:N.161 EDO.6: 6 residues within 4Å: Chain B: Y.260, A.261, R.262, A.263, K.264, P.265 No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: V.247, D.248, P.252, D.253, Y.257 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chowdhury, R. et al., Conservation of the unusual dimeric JmjC fold of JMJD7 from Drosophila melanogaster to humans. Sci Rep (2022)

Release Date

2022-04-27

Peptides

GH14974p: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

GH14974p

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