SMTL ID : 7yxg.1

Drosophila melanogaster JMJD7 (dmJMJD7) in complex with Mn and 2OG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.64 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: AKG.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.7 MN.6: 5 residues within 4Å: Chain B: H.181, D.183, H.284, W.298 Ligands: AKG.7 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.181, B:D.183, B:H.284, H2O.15

2 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.2: 14 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, N.296, W.298 Ligands: MN.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:W.170, A:W.170, A:T.178, A:Y.189, A:V.286 Hydrogen bonds: A:Y.129, A:T.178, A:N.187, A:Y.189, A:Y.189, A:W.298 Water bridges: A:K.196, A:K.196 Salt bridges: A:K.196, A:H.284 AKG.7: 15 residues within 4Å: Chain B: Y.129, W.170, T.178, H.181, D.183, Y.185, N.187, Y.189, K.196, F.198, H.284, V.286, N.296, W.298 Ligands: MN.6 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:W.170, B:W.170, B:T.178, B:Y.189, B:V.286 Hydrogen bonds: B:Y.129, B:T.178, B:T.178, B:N.187, B:Y.189, B:W.298 Water bridges: B:K.196 Salt bridges: B:K.196, B:H.284

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

EDO.3: 7 residues within 4Å: Chain A: K.162, P.163, P.164, D.165, W.298, Y.299, D.300 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.165, A:D.165, A:D.300, A:D.300 EDO.4: 9 residues within 4Å: Chain A: N.50, P.203, N.280, Y.281, L.301, R.306, Y.307, Y.310 Chain B: Y.309 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.280 Water bridges: A:R.306, A:Y.307 EDO.5: 5 residues within 4Å: Chain A: F.160, N.161, K.162, D.302 Chain B: E.45 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.161, A:D.302 EDO.9: 9 residues within 4Å: Chain B: N.50, P.203, N.280, Y.281, L.301, D.304, R.306, Y.307, Y.310 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.50, B:N.280 EDO.10: 6 residues within 4Å: Chain B: S.28, S.29, V.30, L.266, K.267 Ligands: EDO.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.30 EDO.11: 6 residues within 4Å: Chain B: P.37, T.38, A.39, D.154, F.155, Q.158 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.39 Water bridges: B:T.38, B:L.40, B:F.155 EDO.12: 10 residues within 4Å: Chain A: S.48, K.49 Chain B: Y.47, S.48, N.50, E.186, N.280, D.302, D.304, R.306 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.50, B:N.280, B:R.306, A:S.48, A:K.49 Water bridges: B:Y.47, B:N.50 EDO.13: 10 residues within 4Å: Chain B: V.30, V.31, E.32, V.54, R.56, K.267, V.268, R.269 Ligands: MG.8, EDO.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.30, B:K.267 Water bridges: B:E.32 EDO.14: 3 residues within 4Å: Chain B: S.114, E.115, R.118 No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 4 residues within 4Å: Chain B: R.56, V.268, R.269 Ligands: EDO.13 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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