SMTL ID : 5fyz.1

Crystal structure of the catalytic domain of human JARID1B in complex with 3D fragment 2-(2-oxo-2,3-dihydro-1H-indol-3-yl)acetonitrile (N10063a)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 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: 4 residues within 4Å: Chain A: C.415, C.417, C.432, C.434 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.415, A:C.417, A:C.432, A:C.434

1 x NYK: [(3S)-2-oxo-2,3-dihydro-1H-indol-3-yl]acetonitrile(Non-covalent)

NYK.3: 8 residues within 4Å: Chain A: Y.197, F.205, H.208, K.226, W.228, H.296 Ligands: MN.4, DMS.17 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.197, A:Y.197, A:F.205, A:F.205, A:W.228 Hydrogen bonds: A:K.226 pi-Stacking: A:Y.197, A:F.205

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

MN.4: 4 residues within 4Å: Chain A: H.208, E.210, H.296 Ligands: NYK.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.208, A:E.210, A:H.296, H2O.7, H2O.8

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

PO4.5: 3 residues within 4Å: Chain A: H.331, K.403, H.427 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.331, A:H.427

12 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 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.7: 8 residues within 4Å: Chain A: F.60, G.135, A.136, D.137, F.143, L.196, Y.197, V.198 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.135, A:V.198 EDO.8: 5 residues within 4Å: Chain A: R.375, S.386, L.441, Y.443, T.446 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.375 EDO.9: 7 residues within 4Å: Chain A: R.321, D.339, M.367, D.370, E.371, L.374 Ligands: EDO.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.321, A:D.339, A:E.371 EDO.10: 4 residues within 4Å: Chain A: P.7, P.276, V.277, Y.278 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.278 EDO.11: 8 residues within 4Å: Chain A: D.397, E.398, R.399, Q.400, V.402, G.420, L.421, L.422 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.397, A:Q.400, A:L.422, A:L.422 EDO.12: 4 residues within 4Å: Chain A: G.233, Y.234, R.293, L.319 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.293 Water bridges: A:Y.234 EDO.13: 4 residues within 4Å: Chain A: R.379, V.383, I.384, L.441 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.379 EDO.14: 2 residues within 4Å: Chain A: H.273, E.274 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.273 EDO.15: 5 residues within 4Å: Chain A: K.429, E.430, L.431, C.432, S.433 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.429 Water bridges: A:E.430, A:L.431 EDO.16: 7 residues within 4Å: Chain A: E.340, C.343, K.344, E.392, F.409, R.444, Y.445 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:C.343, A:E.392, A:R.444, A:Y.445 EDO.21: 1 residues within 4Å: Chain A: L.422 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.420

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

DMS.17: 9 residues within 4Å: Chain A: Q.65, Q.73, T.74, V.76, Y.134, S.204, F.205, C.206 Ligands: NYK.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.206 DMS.18: 7 residues within 4Å: Chain A: W.195, Y.197, E.210, S.216, A.308, V.309, N.310 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.310 Water bridges: A:N.310 Salt bridges: A:E.210 DMS.19: 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

1 x NA: SODIUM ION(Non-functional Binders)

NA.20: 6 residues within 4Å: Chain A: L.67, N.68, L.122, V.123, T.125, E.128 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.67

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 N10063A. 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

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