SMTL ID : 5lwb.1

Crystal structure of human JARID1B in complex with S40650a

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.39 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

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

MN.2: 6 residues within 4Å: Chain A: L.67, N.68, L.122, V.123, T.125, E.128 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:L.122, A:T.125, A:E.128, H2O.3 MN.12: 4 residues within 4Å: Chain A: H.208, E.210, H.296 Ligands: 79H.14 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.208, A:E.210, A:H.296, H2O.1, H2O.2 MN.13: 2 residues within 4Å: Chain A: H.331, H.427 No protein-ligand interaction detected (PLIP)

4 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: 3 residues within 4Å: Chain A: G.233, Y.234, R.293 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.293 Water bridges: A:Y.234 EDO.5: 4 residues within 4Å: Chain A: R.379, V.383, I.384, L.441 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.375, A:R.379, A:I.384 EDO.6: 2 residues within 4Å: Chain A: V.107, H.108 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.108

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

DMS.7: 7 residues within 4Å: Chain A: I.209, W.213, E.240, H.326, Y.327, L.330, R.332 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.240 DMS.8: 7 residues within 4Å: Chain A: W.195, Y.197, E.210, S.216, V.309, N.310 Ligands: 79H.14 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.197 Salt bridges: A:E.210 DMS.9: 8 residues within 4Å: Chain A: F.60, G.135, A.136, D.137, F.143, L.196, Y.197, V.198 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.137, A:V.198 pi-Cation interactions: A:F.143 DMS.10: 3 residues within 4Å: Chain A: M.2, L.4, N.268 No protein-ligand interaction detected (PLIP) DMS.11: 6 residues within 4Å: Chain A: F.51, A.52, G.144, S.145, G.146, F.305 No protein-ligand interaction detected (PLIP)

1 x 79H: 5-[1-[2-(dimethylamino)ethyl]pyrazol-4-yl]-7-oxidanylidene-6-propan-2-yl-6~{H}-pyrazolo[1,5-a]pyrimidine-3-carbonitrile

79H.14: 20 residues within 4Å: Chain A: Q.65, T.74, R.75, Y.134, G.135, A.136, Y.197, V.198, S.203, S.204, F.205, C.206, H.208, N.218, K.226, V.262, H.296, N.300 Ligands: DMS.8, MN.12 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.134, A:Y.134, A:Y.197, A:Y.197 Hydrogen bonds: A:C.206, A:N.218, A:N.300 Water bridges: A:Y.197, A:Y.197, A:Y.197, A:K.226 pi-Stacking: A:Y.197, A:Y.197, A:F.205

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Srikannathasan, V., Crystal structure of human JARID1B in complex with S40650a. to be published

Release Date

2016-10-26

Peptides

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

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