SMTL ID : 5fyb.1

Crystal structure of the catalytic domain of human JARID1B in complex with MC1648

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 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

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

MN.3: 4 residues within 4Å: Chain A: H.208, E.210, H.296 Ligands: 77J.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.10 MN.4: 2 residues within 4Å: Chain A: H.331, H.427 No protein-ligand interaction detected (PLIP) MN.5: 2 residues within 4Å: Chain A: V.107, H.108 No protein-ligand interaction detected (PLIP) MN.6: 2 residues within 4Å: Chain A: S.253, H.331 No protein-ligand interaction detected (PLIP)

2 x 77J: N-hydroxy-3-[(6-oxo-4-phenyl-1,6-dihydropyrimidin-2-yl)sulfanyl]propanamide(Non-covalent)

77J.7: 7 residues within 4Å: Chain A: E.8, C.9, P.10, V.11, F.12, I.32, T.36 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.10, A:T.36 Hydrogen bonds: A:V.11 77J.8: 16 residues within 4Å: Chain A: V.76, Y.134, Y.197, F.205, H.208, E.210, S.216, N.218, K.226, W.228, H.296, N.300 Ligands: MN.3, EDO.17, DMS.27, DMS.28 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:V.76, A:Y.134, A:Y.197, A:F.205, A:F.205, A:W.228 Hydrogen bonds: A:S.216, A:N.218, A:N.218, A:K.226, A:N.300 Water bridges: A:G.199, A:K.226 pi-Stacking: A:Y.197, A:F.205

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

EDO.9: 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.10: 5 residues within 4Å: Chain A: R.375, S.386, L.441, Y.443, T.446 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: R.321, D.339, M.367, E.371, L.374 Ligands: EDO.23 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: P.7, P.276, V.277, Y.278 Ligand excluded by PLIP EDO.13: 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.14: 4 residues within 4Å: Chain A: G.233, Y.234, R.293, L.319 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: R.379, V.383, I.384, L.441 Ligand excluded by PLIP EDO.16: 1 residues within 4Å: Chain A: H.273 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain A: V.76, W.195, Y.197 Ligands: 77J.8, DMS.28 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: D.96, A.97, S.100, V.107 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain A: L.114, K.117, E.118 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain A: E.387, K.440, R.442 Ligand excluded by PLIP EDO.21: 1 residues within 4Å: Chain A: M.389 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain A: P.5, P.6, P.7, M.271 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain A: V.324, R.328, T.406 Ligands: EDO.11 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain A: K.429, E.430, C.432, S.433 Ligand excluded by PLIP

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

DMS.25: 6 residues within 4Å: Chain A: E.340, K.344, S.347, E.392, F.409, Y.445 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.340 Salt bridges: A:E.392 DMS.26: 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.27: 8 residues within 4Å: Chain A: Q.65, Q.73, T.74, Y.134, S.204, F.205, C.206 Ligands: 77J.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.206 DMS.28: 9 residues within 4Å: Chain A: W.195, Y.197, E.210, S.216, A.308, V.309, N.310 Ligands: 77J.8, EDO.17 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.210

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 Mc1648. To be Published

Release Date

2017-03-29

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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