SMTL ID : 5fy4.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 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

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

MN.2: 5 residues within 4Å: Chain A: L.67, L.122, V.123, T.125, E.128 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:L.67, A:L.122, A:T.125, A:E.128, H2O.2 MN.3: 2 residues within 4Å: Chain A: H.331, H.427 No protein-ligand interaction detected (PLIP) MN.11: 2 residues within 4Å: Chain A: V.107, H.108 No protein-ligand interaction detected (PLIP) MN.12: 4 residues within 4Å: Chain A: H.208, E.210, H.296 Ligands: FUM.14 6 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:H.208, A:E.210, A:H.296, H2O.2, H2O.5, FUM.14 MN.13: 5 residues within 4Å: Chain A: I.209, W.213, H.326, Y.327, R.332 No protein-ligand interaction detected (PLIP)

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

EDO.4: 5 residues within 4Å: Chain A: R.375, S.386, L.441, T.446 Ligands: EDO.9 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.375 EDO.5: 6 residues within 4Å: Chain A: R.321, D.339, M.367, D.370, E.371, L.374 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.321, A:E.371 Water bridges: A:R.321, A:D.339, A:D.339, A:D.339, A:D.370 EDO.6: 4 residues within 4Å: Chain A: P.7, P.276, V.277, Y.278 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.277, A:V.277 EDO.7: 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.8: 4 residues within 4Å: Chain A: G.233, Y.234, R.293, L.319 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.293 EDO.9: 5 residues within 4Å: Chain A: R.379, V.383, I.384, L.441 Ligands: EDO.4 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.379 EDO.10: 1 residues within 4Å: Chain A: H.273 No protein-ligand interaction detected (PLIP)

1 x FUM: FUMARIC ACID(Non-covalent)

FUM.14: 9 residues within 4Å: Chain A: Y.134, Y.197, F.205, H.208, N.218, K.226, W.228, H.296 Ligands: MN.12 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.197, A:F.205, A:W.228 Hydrogen bonds: A:Y.134, A:N.218 Water bridges: A:R.75, A:R.75 Salt bridges: A:H.208, A:K.226, A:H.296

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 Succinate. To be Published

Release Date

2017-03-22

Peptides

LYSINE-SPECIFIC DEMETHYLASE 5B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

LYSINE-SPECIFIC DEMETHYLASE 5B

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