SMTL ID : 5fyt.1

Crystal structure of the catalytic domain of human JARID1B in complex with 3D fragment (5-fluoro-2-oxo-2,3-dihydro-1H-indol-3-yl)acetic acid (N09996a)

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

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

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

1 x WQS: 2-[(3S)-5-fluoranyl-2-oxidanylidene-1,3-dihydroindol-3-yl]ethanoic acid(Non-covalent)

WQS.4: 10 residues within 4Å: Chain A: Y.197, F.205, H.208, N.218, K.226, W.228, H.296, A.308 Ligands: MN.3, DMS.23 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.197, A:F.205, A:F.205, A:F.205, A:W.228 Hydrogen bonds: A:N.218 Salt bridges: A:H.208, A:H.296 pi-Stacking: A:Y.197, A:F.205

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

EDO.5: 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.6: 5 residues within 4Å: Chain A: R.375, S.386, L.441, Y.443, T.446 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: R.321, D.339, M.367, E.371, L.374 Ligands: EDO.16 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: P.7, P.276, V.277, Y.278 Ligand excluded by PLIP EDO.9: 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.10: 4 residues within 4Å: Chain A: G.233, Y.234, R.293, L.319 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: R.379, V.383, I.384, D.385, L.441 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: D.96, A.97, S.100, V.107 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: L.114, K.117, E.118 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain A: E.387, K.440, R.442 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain A: L.4, P.5, P.6, P.7, M.271 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain A: E.371, L.374, M.410, S.411, C.424, L.425 Ligands: EDO.7 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: E.430, L.431, C.432, S.433 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: W.16, W.47, E.162, Y.163, S.166 Ligand excluded by PLIP EDO.19: 1 residues within 4Å: Chain A: R.388 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain A: I.209, W.213, H.326, Y.327, L.330 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain A: T.377, L.425, H.426, H.427, V.428 Ligand excluded by PLIP EDO.27: 1 residues within 4Å: Chain A: L.422 Ligand excluded by PLIP

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

DMS.22: 6 residues within 4Å: Chain A: E.340, C.343, K.344, E.392, F.409, Y.445 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.445 Water bridges: A:E.340 Salt bridges: A:E.392 DMS.23: 8 residues within 4Å: Chain A: Q.65, Q.73, T.74, Y.134, S.204, F.205, C.206 Ligands: WQS.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.206 DMS.24: 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

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

PO4.25: 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

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

CL.26: 5 residues within 4Å: Chain A: L.67, N.68, L.122, T.125, E.128 Ligand excluded by PLIP

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 N09996A. 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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