SMTL ID : 5fyy.1

Crystal structure of the catalytic domain of human JARID1B in complex with Maybridge fragment 3-pyridin-3-ylaniline (N05798a) (ligand modelled based on PANDDA event map)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

monomer

Ligands

2 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 ZN.2: 5 residues within 4Å: Chain A: C.415, C.417, K.418, C.432, C.434 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.415, A:C.432, A:C.434

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 6 residues within 4Å: Chain A: L.67, N.68, L.122, V.123, T.125, E.128 Ligand excluded by PLIP

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

MN.4: 4 residues within 4Å: Chain A: H.208, E.210, H.296 Ligands: N6Y.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.208, A:E.210, A:H.296, H2O.5, H2O.5

1 x N6Y: 3-(pyridin-3-yl)aniline(Non-covalent)

N6Y.5: 12 residues within 4Å: Chain A: V.76, Y.134, Y.197, F.205, H.208, N.218, W.228, H.296 Ligands: MN.4, EDO.17, EDO.18, DMS.24 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.76, A:Y.134, A:F.205, A:W.228 Hydrogen bonds: A:V.76 Water bridges: A:R.75, A:Y.197, A:Y.197 pi-Stacking: A:Y.197, A:F.205

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

EDO.6: 6 residues within 4Å: Chain A: D.339, C.408, F.409, M.410, S.411 Ligands: EDO.9 Ligand excluded by PLIP EDO.7: 8 residues within 4Å: Chain A: F.60, G.135, A.136, D.137, F.143, L.196, Y.197, V.198 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: R.375, S.386, L.441, Y.443, T.446 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain A: R.321, D.339, M.367, D.370, E.371, L.374 Ligands: EDO.6 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: P.7, M.271, P.276, V.277, Y.278 Ligand excluded by PLIP EDO.11: 8 residues within 4Å: Chain A: D.397, E.398, R.399, Q.400, V.402, G.420, L.421, L.422 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: G.233, Y.234, R.293, L.319 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: R.379, V.383, I.384, D.385, L.441 Ligand excluded by PLIP EDO.14: 2 residues within 4Å: Chain A: H.273, E.274 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: L.114, K.117, E.118, R.121 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain A: D.96, A.97, S.100 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain A: R.75, V.76, C.206, H.208 Ligands: N6Y.5, DMS.24 Ligand excluded by PLIP EDO.18: 9 residues within 4Å: Chain A: Y.134, Y.197, G.199, S.203, S.204, F.205, K.226, N.300 Ligands: N6Y.5 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain A: A.72, Q.73, T.74 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain A: T.377, L.425, H.426, H.427, V.428 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain A: W.16, W.47, E.162, Y.163, S.166 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain A: Q.361, K.362, A.365, I.366 Ligand excluded by PLIP EDO.28: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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

DMS.23: 7 residues within 4Å: Chain A: W.195, Y.197, E.210, S.216, A.308, V.309, N.310 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.210 DMS.24: 9 residues within 4Å: Chain A: Q.65, Q.73, T.74, Y.134, S.204, F.205, C.206 Ligands: N6Y.5, EDO.17 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.206 DMS.25: 6 residues within 4Å: Chain A: I.209, W.213, H.326, Y.327, L.330, R.332 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.240 DMS.26: 3 residues within 4Å: Chain A: C.343, K.344, Y.445 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.392

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.27: 3 residues within 4Å: Chain A: H.331, K.403, H.427 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.329 Salt bridges: A:H.331, A:K.403, A:H.427

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nowak, R. et al., Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with N05798A. To be Published

Release Date

2016-03-23

Peptides

LYSINE-SPECIFIC DEMETHYLASE 5B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

LYSINE-SPECIFIC DEMETHYLASE 5B