SMTL ID : 6g5p.1 (1 other biounit)

Crystal structure of human SP100 in complex with bromodomain-focused fragment FM009493b 2,3-Dimethoxy-2,3-dimethyl-2,3-dihydro-1,4-benzodioxin-6-amine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.6, C.9, H.26, C.29 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.6, A:C.9, A:H.26, A:C.29 ZN.2: 4 residues within 4Å: Chain A: C.18, C.21, C.43, C.46 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.18, A:C.21, A:C.43, A:C.46

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.3: 3 residues within 4Å: Chain A: N.103, R.104, Y.149 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.104

3 x EDO: ethane-1,2-diol(Non-functional Binders)

EDO.4: 4 residues within 4Å: Chain A: E.64, S.65, L.68, R.139 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.64, A:R.139 Water bridges: A:R.139, A:R.139 EDO.5: 4 residues within 4Å: Chain A: F.95, P.100, H.145, Y.149 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.145, A:Y.149 Water bridges: A:Y.101 EDO.6: 3 residues within 4Å: Chain A: C.94, A.97, S.98 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.94, A:S.98 Water bridges: A:A.97

1 x EN8: (2~{R},3~{R})-2,3-dimethoxy-2,3-dimethyl-1,4-benzodioxin-6-amine(Non-covalent)

EN8.7: 9 residues within 4Å: Chain A: R.23, F.45, I.48, Q.52, F.82, K.86, N.168, N.171, I.172 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.48 Hydrogen bonds: A:Q.52 Water bridges: A:K.86, A:N.171

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Talon, R.P.H. et al., Identifying small molecule binding sites for epigenetic proteins at domain-domain interfaces. Biorxiv (2018)

Release Date

2018-04-11

Peptides

Nuclear autoantigen Sp-100: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Nuclear autoantigen Sp-100

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