SMTL ID : 3ldb.1

Structure of JMJD6 complexd with ALPHA-KETOGLUTARATE and Fab Fragment.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-1-1-1-mer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: D.50, Q.53, L.54, E.58, R.62 Chain C: S.54 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.50, A:E.58, A:R.62, A:R.62 GOL.2: 2 residues within 4Å: Chain A: D.279, T.280 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.280 GOL.3: 6 residues within 4Å: Chain A: M.1, S.5, K.6, I.9, E.119, S.123 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.5 GOL.4: 3 residues within 4Å: Chain A: R.95, N.96, K.115 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.95, A:N.96 GOL.22: 1 residues within 4Å: Chain B: R.114 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.114, B:R.114

19 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 2 residues within 4Å: Chain A: N.237, P.241 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain A: N.96, Q.97, K.142 Ligand excluded by PLIP SO4.7: 5 residues within 4Å: Chain A: K.100, S.109, K.111, D.134, S.136 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain A: L.147, Y.172, R.173 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain A: T.221, R.222, Q.229 Ligand excluded by PLIP SO4.10: 5 residues within 4Å: Chain A: Q.97, H.140, P.141, K.142, R.143 Ligand excluded by PLIP SO4.11: 5 residues within 4Å: Chain A: K.4, R.8, K.113, K.115, Y.116 Ligand excluded by PLIP SO4.12: 4 residues within 4Å: Chain A: G.165, E.166, K.167, R.168 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain A: P.190, L.191, K.300 Ligand excluded by PLIP SO4.14: 3 residues within 4Å: Chain A: P.214, R.215, E.216 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain A: K.307, R.310, R.314 Ligand excluded by PLIP SO4.16: 5 residues within 4Å: Chain A: G.304, R.305, P.306, K.307, L.308 Ligand excluded by PLIP SO4.17: 5 residues within 4Å: Chain A: W.298, R.310, Y.313, D.328, D.331 Ligand excluded by PLIP SO4.23: 4 residues within 4Å: Chain B: Q.48, S.49, K.51 Chain C: Q.110 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain B: S.71, G.72, D.76, T.78 Ligand excluded by PLIP SO4.25: 5 residues within 4Å: Chain B: Q.43, K.51, L.53, V.64, P.65 Ligand excluded by PLIP SO4.26: 1 residues within 4Å: Chain C: R.71 Ligand excluded by PLIP SO4.27: 10 residues within 4Å: Chain B: L.166, Q.167, S.168, S.182, T.184 Chain C: P.174, V.176, S.183, L.184, S.185 Ligand excluded by PLIP SO4.28: 1 residues within 4Å: Chain C: Q.81 Ligand excluded by PLIP

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

AKG.18: 9 residues within 4Å: Chain A: W.174, T.184, D.189, N.197, K.204, V.275, T.285, N.287 Ligands: FE.19 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.197, A:T.285, A:N.287 Salt bridges: A:H.187, A:K.204

1 x FE: FE (III) ION(Non-covalent)

FE.19: 4 residues within 4Å: Chain A: H.187, D.189, H.273 Ligands: AKG.18 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.187, A:H.273

2 x HG: MERCURY (II) ION(Non-covalent)

HG.20: 3 residues within 4Å: Chain A: W.206, C.207, W.235 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.207 HG.21: 3 residues within 4Å: Chain A: C.101, M.112, L.130 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.101

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hong, X. et al., Interaction of JMJD6 with single-stranded RNA. Proc.Natl.Acad.Sci.USA (2010)

Release Date

2010-08-04

Peptides

Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6: A
antibody Fab fragment light chain: B
antibody Fab fragment heavy chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6

antibody Fab fragment light chain

antibody Fab fragment heavy chain

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