SMTL ID : 5tbp.3 (2 other biounits)

Crystal Structure of RXR-alpha ligand binding domain complexed with synthetic modulator K8003

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

3 x 7A4: [(1Z)-5-fluoro-2-methyl-1-{[4-(propan-2-yl)phenyl]methylidene}-1H-inden-3-yl]acetic acid(Non-covalent)

7A4.1: 16 residues within 4Å: Chain A: C.51, A.54, D.55, L.58, R.84, W.87, L.215 Chain B: V.47, C.51, L.218, F.221, I.229, F.232, L.233 Ligands: GOL.2, 7A4.6 13 PLIP interactions: 8 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:V.47, B:F.221, B:F.221, B:I.229, B:I.229, B:F.232, A:D.55, A:L.58, A:R.84, A:W.87 pi-Stacking: B:F.221, B:F.221 Hydrogen bonds: A:W.87 7A4.5: 15 residues within 4Å: Chain A: V.47, L.218, F.221, K.222, I.229, L.233 Chain B: A.54, Q.57, L.58, L.61, L.83, R.84, W.87, L.91 Ligands: 7A4.6 11 PLIP interactions: 3 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:V.47, A:F.221, B:A.54, B:Q.57, B:L.58, B:L.91 Salt bridges: A:K.222 Hydrogen bonds: B:W.87 pi-Stacking: B:W.87, B:W.87, B:W.87 7A4.6: 17 residues within 4Å: Chain B: I.50, A.53, A.54, Q.57, L.91, F.95, R.98, L.108, A.109, T.110, F.220, F.221, L.223, I.224 Ligands: 7A4.1, GOL.2, 7A4.5 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.50, B:A.54, B:F.95, B:L.108, B:L.108, B:A.109, B:F.220, B:F.220, B:F.221 Hydrogen bonds: B:Q.57, B:A.109 Salt bridges: B:R.98

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: I.50, C.51, A.54, W.87, L.218, F.221 Ligands: 7A4.1, 7A4.6 No protein-ligand interaction detected (PLIP)

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 5 residues within 4Å: Chain A: R.16, K.66, R.67 Chain B: H.241, Q.242 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Q.242 Salt bridges: A:R.16, A:R.67 ACT.4: 7 residues within 4Å: Chain A: Q.57, L.91, S.94, F.95, R.98, L.108, A.109 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.95 Hydrogen bonds: A:Q.57, A:A.109 Salt bridges: A:R.98 ACT.7: 6 residues within 4Å: Chain B: D.141, M.142, Q.143, Y.190, Q.193, R.196 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.190 Hydrogen bonds: B:Q.143, B:Q.193 Salt bridges: B:R.196

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, L. et al., Modulation of nongenomic activation of PI3K signalling by tetramerization of N-terminally-cleaved RXR alpha. Nat Commun (2017)

Release Date

2017-08-09

Peptides

Retinoic acid receptor RXR-alpha: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

Retinoic acid receptor RXR-alpha

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