- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.04 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x FE: FE (III) ION(Non-covalent)
- 2 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)
AKG.2: 10 residues within 4Å:- Chain A: Y.131, F.133, T.184, H.187, D.189, N.197, K.204, H.273, V.275
- Ligands: FE.1
7 PLIP interactions:7 interactions with chain A- Hydrophobic interactions: A:F.133, A:V.275
- Hydrogen bonds: A:T.184, A:T.184, A:N.197
- Salt bridges: A:H.187, A:K.204
AKG.13: 10 residues within 4Å:- Chain B: Y.131, F.133, T.184, H.187, D.189, N.197, K.204, H.273, V.275
- Ligands: FE.12
7 PLIP interactions:7 interactions with chain B- Hydrophobic interactions: B:F.133, B:V.275
- Hydrogen bonds: B:Y.131, B:N.197
- Water bridges: B:T.285
- Salt bridges: B:H.187, B:K.204
- 1 x NA: SODIUM ION(Non-functional Binders)
- 10 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.4: 3 residues within 4Å:- Chain A: S.109, K.111, S.136
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:S.109, A:S.136, A:S.136
- Water bridges: A:S.109, A:S.136, A:S.136
PO4.5: 7 residues within 4Å:- Chain A: N.74, A.75, Q.76, E.77, W.79, K.151, P.153
7 PLIP interactions:7 interactions with chain A- Hydrogen bonds: A:A.75, A:E.77, A:W.79
- Water bridges: A:K.151, A:K.151, A:K.154
- Salt bridges: A:K.151
PO4.6: 5 residues within 4Å:- Chain A: G.304, R.305, P.306, K.307, L.308
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:K.307, A:L.308
- Salt bridges: A:R.305
PO4.7: 3 residues within 4Å:- Chain A: K.91, R.95, E.119
2 PLIP interactions:2 interactions with chain A- Salt bridges: A:K.91, A:R.95
PO4.8: 4 residues within 4Å:- Chain A: K.4, R.8, K.113, Y.116
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:Y.116
- Salt bridges: A:R.8, A:K.113
PO4.14: 3 residues within 4Å:- Chain B: S.55, V.56, K.154
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:V.56
- Salt bridges: B:K.154
PO4.15: 3 residues within 4Å:- Chain B: S.109, K.111, S.136
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:S.109, B:S.136, B:S.136, B:S.136
- Salt bridges: B:K.100
PO4.16: 4 residues within 4Å:- Chain B: R.305, P.306, K.307, L.308
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:R.305, B:K.307, B:L.308
- Salt bridges: B:R.305
PO4.17: 3 residues within 4Å:- Chain B: R.8, K.113, Y.116
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:Y.116
- Water bridges: B:R.8
- Salt bridges: B:R.8, B:K.113
PO4.18: 7 residues within 4Å:- Chain A: P.295, S.329, V.330, Q.333
- Chain B: R.65, S.291, L.326
3 PLIP interactions:1 interactions with chain B, 2 interactions with chain A- Salt bridges: B:R.65
- Hydrogen bonds: A:S.329, A:Q.333
- 2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)
- 3 x GOL: GLYCEROL(Non-functional Binders)
GOL.11: 8 residues within 4Å:- Chain A: Y.67, T.211, G.269, G.270, V.296
- Chain B: E.61, R.65, P.66
3 PLIP interactions:3 interactions with chain A- Water bridges: A:Y.67, A:T.211, A:W.271
GOL.19: 8 residues within 4Å:- Chain B: A.75, Q.76, E.77, W.79, K.151, V.152, P.153, K.154
6 PLIP interactions:6 interactions with chain B- Hydrogen bonds: B:A.75, B:E.77, B:E.77, B:K.154
- Water bridges: B:K.151, B:K.151
GOL.20: 8 residues within 4Å:- Chain B: R.17, W.26, S.128, P.129, L.130, Y.131, G.183, E.231
7 PLIP interactions:7 interactions with chain B- Hydrogen bonds: B:R.17, B:G.183, B:E.231
- Water bridges: B:Y.131, B:G.183, B:E.231, B:E.231
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Islam, M.S. et al., Biochemical and structural investigations clarify the substrate selectivity of the 2-oxoglutarate oxygenase JMJD6. J.Biol.Chem. (2019)
- Release Date
- 2019-04-03
- Peptides
- Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.04 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x FE: FE (III) ION(Non-covalent)
- 2 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)
- 1 x NA: SODIUM ION(Non-functional Binders)
- 10 x PO4: PHOSPHATE ION(Non-functional Binders)
- 2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)
- 3 x GOL: GLYCEROL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Islam, M.S. et al., Biochemical and structural investigations clarify the substrate selectivity of the 2-oxoglutarate oxygenase JMJD6. J.Biol.Chem. (2019)
- Release Date
- 2019-04-03
- Peptides
- Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B