SMTL ID : 5lw9.1

Crystal structure of human JARID1B in complex with S40563a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.401, C.404, C.424, H.427 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.401, A:C.404, A:C.424, A:H.427

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

MN.2: 5 residues within 4Å: Chain A: L.67, N.68, L.122, T.125, E.128 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:L.67, A:T.125 MN.9: 4 residues within 4Å: Chain A: H.208, E.210, H.296 Ligands: 5UJ.8 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.208, A:E.210, A:H.296, H2O.3

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

EDO.3: 5 residues within 4Å: Chain A: D.339, C.408, F.409, M.410, S.411 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.339, A:F.409, A:M.410, A:S.411, A:S.411 Water bridges: A:D.339 EDO.4: 4 residues within 4Å: Chain A: G.233, Y.234, R.293, L.319 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.234, A:P.292

3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.5: 8 residues within 4Å: Chain A: I.209, W.213, E.240, R.293, H.326, Y.327, L.330, R.332 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.327 Salt bridges: A:E.240 DMS.6: 8 residues within 4Å: Chain A: W.195, Y.197, E.210, S.216, A.308, V.309, N.310 Ligands: 5UJ.8 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.310 Salt bridges: A:E.210 DMS.7: 6 residues within 4Å: Chain A: R.75, F.205, C.206, H.208, V.262 Ligands: 5UJ.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.206 pi-Cation interactions: A:H.208

1 x 5UJ: 8-[4-[2-[4-[3,5-bis(chloranyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one(Non-covalent)

5UJ.8: 18 residues within 4Å: Chain A: R.75, V.76, Y.134, D.137, I.188, G.190, W.195, Y.197, F.205, H.208, E.210, N.218, K.226, W.228, H.296 Ligands: DMS.6, DMS.7, MN.9 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.76, A:W.195, A:W.228 Hydrogen bonds: A:Y.134, A:Y.134, A:N.218 Salt bridges: A:D.137 pi-Stacking: A:F.205

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

srikannathasan, v., Crystal structure of human JARID1B in complex with S40563a. to be published

Release Date

2016-09-28

Peptides

Lysine-specific demethylase 5B,Lysine-specific demethylase 5B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysine-specific demethylase 5B,Lysine-specific demethylase 5B

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