SMTL ID : 6ydv.1 (1 other biounit)

Crystal Structure of the Jmjc Domain of Human JMJD1B in complex with FM001511a from the DSPL fragment library

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

monomer

Ligands

1 x ONQ: ~{N}-(2-azanyl-2-oxidanylidene-ethyl)-4-methoxy-benzamide(Non-covalent)

ONQ.1: 13 residues within 4Å: Chain A: C.30, D.31, R.33, D.238, A.239, D.240, A.262, K.264, D.265, Q.313, G.314, W.315, A.316 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:R.33, A:Q.313, A:Q.313 Hydrogen bonds: A:R.33, A:D.238, A:G.314, A:A.316 Water bridges: A:R.33, A:D.240, A:Q.313, A:Q.313, A:Q.313 pi-Stacking: A:W.315, A:W.315 pi-Cation interactions: A:R.33

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

CL.2: 5 residues within 4Å: Chain A: W.46, L.155, P.156, E.157, Y.158 Ligand excluded by PLIP CL.3: 4 residues within 4Å: Chain A: M.142, P.143, T.144, R.145 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: K.128, T.201, N.202, Q.294 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: A.263, H.353, H.356 Ligand excluded by PLIP

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

MN.6: 3 residues within 4Å: Chain A: H.204, D.206, H.333 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.204, A:D.206

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Snee, M. et al., Crystal Structure of the Jmjc Domain of Human JMJD1B in complex with FM001511a from the DSPL fragment library. To Be Published

Release Date

2020-05-06

Peptides

JMJD1B protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

JMJD1B protein

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