SMTL ID : 3kmz.3 (2 other biounits)

Crystal structure of RARalpha ligand binding domain in complex with the inverse agonist BMS493 and a corepressor fragment

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-2-2-mer

Ligands

2 x EQO: 4-{(E)-2-[5,5-dimethyl-8-(phenylethynyl)-5,6-dihydronaphthalen-2-yl]ethenyl}benzoic acid(Non-covalent)

EQO.1: 21 residues within 4Å: Chain A: F.44, W.70, F.73, S.74, L.76, S.77, T.78, C.80, I.81, L.111, L.114, I.115, I.118, R.121, F.131, S.132, F.147, G.236 Chain B: L.5, H.8, I.9 18 PLIP interactions: 15 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:W.70, A:F.73, A:F.73, A:I.81, A:L.111, A:L.114, A:L.114, A:I.115, A:I.118, A:F.131, A:F.131, A:F.147, A:F.147, B:L.5, B:L.5, B:I.9 Hydrogen bonds: A:S.132 Salt bridges: A:R.121 EQO.7: 21 residues within 4Å: Chain C: F.44, W.70, F.73, S.74, L.76, S.77, T.78, C.80, I.81, L.111, L.114, I.115, I.118, R.121, F.131, S.132, F.147, G.236 Chain D: L.5, H.8, I.9 18 PLIP interactions: 15 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:W.70, C:F.73, C:F.73, C:I.81, C:L.111, C:L.114, C:L.114, C:I.115, C:I.118, C:F.131, C:F.131, C:F.147, C:F.147, D:L.5, D:L.5, D:I.9 Hydrogen bonds: C:S.132 Salt bridges: C:R.121

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 10 residues within 4Å: Chain A: L.164, E.165, M.166, E.170, V.208, R.211, R.212, R.215, M.218, M.222 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.165, A:V.208, A:R.212, A:R.212, A:R.215 GOL.3: 7 residues within 4Å: Chain A: S.64, L.65, W.70, G.146, R.239, I.241, T.242 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.64, A:G.146, A:R.239, A:T.242 Water bridges: A:G.148 GOL.4: 6 residues within 4Å: Chain A: T.54, T.55, N.56, S.59, N.138, Q.141 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.54, A:N.56, A:S.59, A:S.59, A:Q.141 GOL.5: 9 residues within 4Å: Chain A: K.205, R.209, P.216, H.217, F.219, P.220 Chain C: K.205, F.219 Ligands: GOL.11 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:K.205, A:R.209, A:R.209, A:H.217 Water bridges: C:E.202, C:K.205, A:M.218 GOL.6: 7 residues within 4Å: Chain A: A.108, L.111, D.112, R.230, S.233, A.234, A.237 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.112, A:R.230, A:R.230 Water bridges: A:L.111 GOL.8: 10 residues within 4Å: Chain C: L.164, E.165, M.166, E.170, V.208, R.211, R.212, R.215, M.218, M.222 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.165, C:V.208, C:R.212, C:R.212, C:R.215 GOL.9: 7 residues within 4Å: Chain C: S.64, L.65, W.70, G.146, R.239, I.241, T.242 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.64, C:G.146, C:R.239, C:T.242 Water bridges: C:G.148 GOL.10: 6 residues within 4Å: Chain C: T.54, T.55, N.56, S.59, N.138, Q.141 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.54, C:N.56, C:S.59, C:S.59, C:Q.141 GOL.11: 9 residues within 4Å: Chain A: K.205, F.219 Chain C: K.205, R.209, P.216, H.217, F.219, P.220 Ligands: GOL.5 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.209, C:R.209, C:H.217, A:K.205 Water bridges: C:M.218 GOL.12: 7 residues within 4Å: Chain C: A.108, L.111, D.112, R.230, S.233, A.234, A.237 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.112, C:R.230, C:R.230 Water bridges: C:L.111

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

le Maire, A. et al., A unique secondary-structure switch controls constitutive gene repression by retinoic acid receptor. Nat.Struct.Mol.Biol. (2010)

Release Date

2010-06-02

Peptides

Retinoic acid receptor alpha: AC
Nuclear receptor corepressor 1: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
D

D
D

Retinoic acid receptor alpha

Nuclear receptor corepressor 1

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