SMTL ID : 5fv3.1

Crystal structure of human JARID1B construct c2 in complex with N- Oxalylglycine.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.37 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.406, C.409, C.429, H.432 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.406, A:C.409, A:C.429, A:H.432

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

DMS.2: 4 residues within 4Å: Chain A: E.345, K.349, E.397, Y.450 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.397 DMS.3: 7 residues within 4Å: Chain A: W.200, Y.202, E.215, A.313, V.314, N.315 Ligands: OGA.17 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.215

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

MN.4: 4 residues within 4Å: Chain A: H.213, E.215, H.301 Ligands: OGA.17 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.213, A:E.215, A:H.301, H2O.3 MN.5: 2 residues within 4Å: Chain A: H.336, H.432 No protein-ligand interaction detected (PLIP)

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.6: 13 residues within 4Å: Chain A: I.214, W.218, E.245, L.255, F.256, Q.259, L.266, V.267, Y.300, H.331, Y.332, L.335, R.337 6 PLIP interactions: 6 interactions with chain A Water bridges: A:W.212, A:Y.332 Salt bridges: A:E.245, A:H.331, A:R.337 pi-Cation interactions: A:F.256

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

EDO.7: 6 residues within 4Å: Chain A: D.344, C.413, F.414, M.415, S.416 Ligands: EDO.9 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.344, A:F.414, A:M.415, A:S.416, A:S.416 Water bridges: A:D.344 EDO.8: 4 residues within 4Å: Chain A: R.380, L.446, Y.448, T.451 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.380, A:R.380 EDO.9: 6 residues within 4Å: Chain A: R.326, D.344, M.372, D.375, E.376 Ligands: EDO.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.326, A:D.344, A:M.372, A:E.376 EDO.10: 5 residues within 4Å: Chain A: P.7, M.276, P.281, V.282, Y.283 No protein-ligand interaction detected (PLIP) EDO.11: 8 residues within 4Å: Chain A: D.402, E.403, R.404, Q.405, V.407, G.425, L.426, L.427 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.402, A:Q.405, A:L.427, A:L.427 EDO.12: 3 residues within 4Å: Chain A: G.238, Y.239, R.298 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.298 EDO.13: 6 residues within 4Å: Chain A: R.384, V.388, I.389, D.390, S.391, L.446 No protein-ligand interaction detected (PLIP) EDO.14: 4 residues within 4Å: Chain A: A.20, W.47, E.167, S.171 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.20, A:E.167, A:G.172 EDO.15: 7 residues within 4Å: Chain A: Y.139, Y.202, S.208, S.209, K.231, N.305 Ligands: OGA.17 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.209, A:K.231, A:N.305 Water bridges: A:K.231

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

CL.16: 6 residues within 4Å: Chain A: L.67, N.68, L.127, V.128, T.130, E.133 Ligand excluded by PLIP

1 x OGA: N-OXALYLGLYCINE(Non-covalent)

OGA.17: 13 residues within 4Å: Chain A: Y.202, F.210, H.213, E.215, S.221, N.223, K.231, W.233, H.301, A.313 Ligands: DMS.3, MN.4, EDO.15 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.221, A:N.223 Salt bridges: A:K.231, A:H.301

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johansson, C. et al., Structural Analysis of Human Kdm5B Guides Histone Demethylase Inhibitor Development. Nat.Chem.Biol. (2016)

Release Date

2016-02-17

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