SMTL ID : 7yxl.1

Drosophila melanogaster JMJD7 (dmJMJD7) in complex with Mn and N-oxalyl-D-phenylalanine (NOFD)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 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: NDF.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.181, A:D.183, A:H.284, H2O.4 MN.11: 5 residues within 4Å: Chain B: H.181, D.183, H.284, W.298 Ligands: NDF.13 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.181, B:D.183, B:H.284, H2O.9

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 7 residues within 4Å: Chain A: S.246, V.247, D.248, S.251, P.252, D.253, Y.257 No protein-ligand interaction detected (PLIP) MG.12: 6 residues within 4Å: Chain B: V.247, D.248, S.251, P.252, D.253, Y.257 No protein-ligand interaction detected (PLIP)

2 x NDF: N-(CARBOXYCARBONYL)-D-PHENYLALANINE(Non-covalent)

NDF.3: 15 residues within 4Å: Chain A: D.92, Q.131, N.168, W.170, T.178, H.181, D.183, N.187, Y.189, K.196, H.284, V.286, N.296, W.298 Ligands: MN.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.298 Hydrogen bonds: A:T.178, A:T.178, A:N.187, A:Y.189, A:N.296, A:W.298 Salt bridges: A:K.196, A:H.284 NDF.13: 15 residues within 4Å: Chain B: N.168, W.170, T.178, H.181, D.183, N.187, Y.189, K.196, H.284, V.286, Q.288, N.296, W.298 Ligands: MN.11, EDO.14 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.298 Hydrogen bonds: B:T.178, B:N.187, B:Y.189, B:W.298 Salt bridges: B:K.196, B:H.284

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

EDO.4: 6 residues within 4Å: Chain A: K.162, P.163, P.164, D.165, Y.299, D.300 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.165, A:D.300 EDO.5: 6 residues within 4Å: Chain A: T.68, P.69, K.70, Y.71, V.117, K.291 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.291 Water bridges: A:D.121, A:D.121 EDO.6: 7 residues within 4Å: Chain A: H.181, K.182, R.211, E.243, W.244, V.245, F.283 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.182, A:K.182 Water bridges: A:M.180, A:E.314 EDO.7: 6 residues within 4Å: Chain A: R.211, G.212, I.213, E.243, T.317, S.318 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.317 EDO.8: 12 residues within 4Å: Chain A: Y.47, S.48, N.50, E.186, N.280, L.301, D.302, D.304, R.306 Chain B: S.48, K.49 Ligands: ACT.9 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.47, A:N.50, A:N.280, A:D.304, A:R.306 Water bridges: A:N.50, A:N.50 EDO.14: 9 residues within 4Å: Chain B: N.168, F.169, W.170, Y.189, K.196, A.294, V.295, N.296 Ligands: NDF.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.189, B:Y.189, B:N.296 EDO.15: 7 residues within 4Å: Chain B: V.30, E.32, V.54, R.56, K.267, V.268, R.269 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.267 Water bridges: B:V.30, B:V.30, B:E.32, B:E.32, B:K.267

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.9: 10 residues within 4Å: Chain A: N.50, P.203, N.280, Y.281, R.306, Y.307, Y.310 Chain B: S.305, Y.309 Ligands: EDO.8 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.203, A:R.306, B:Y.309 Hydrogen bonds: A:R.306 Water bridges: A:N.280 ACT.10: 5 residues within 4Å: Chain A: F.160, N.161, D.302 Chain B: R.44, E.45 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.161 Salt bridges: A:K.162

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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