SMTL ID : 5tbp.1 (2 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-tetramer

Ligands

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

7A4.1: 15 residues within 4Å: Chain A: A.54, Q.57, L.58, L.61, L.83, R.84, W.87, L.91 Chain C: V.47, L.218, F.221, K.222, I.229, L.233 Ligands: 7A4.2 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:A.54, A:Q.57, A:L.58, A:L.58, A:R.84, A:W.87, A:W.87, C:F.221 Hydrogen bonds: A:W.87 Salt bridges: A:R.84, C:K.222 pi-Stacking: A:W.87, A:W.87 7A4.2: 18 residues within 4Å: Chain A: V.47, I.50, C.51, A.53, A.54, Q.57, L.91, F.95, R.98, L.108, A.109, T.110, F.220, F.221, I.224 Ligands: 7A4.1, 7A4.3, GOL.13 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.50, A:A.54, A:F.95, A:L.108, A:L.108, A:A.109, A:F.220, A:I.224 Hydrogen bonds: A:Q.57, A:A.109 Salt bridges: A:R.98 7A4.3: 16 residues within 4Å: Chain A: V.47, C.51, L.218, F.221, I.229, F.232, L.233 Chain C: C.51, A.54, D.55, L.58, R.84, W.87, L.215 Ligands: 7A4.2, GOL.13 12 PLIP interactions: 6 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: C:A.54, C:D.55, C:L.58, C:R.84, C:W.87, A:V.47, A:F.221, A:I.229, A:F.232 Hydrogen bonds: C:W.87 pi-Stacking: A:F.221, A:F.221 7A4.9: 16 residues within 4Å: Chain B: C.51, A.54, D.55, L.58, R.84, W.87, L.215 Chain D: V.47, C.51, L.218, F.221, I.229, F.232, L.233 Ligands: GOL.10, 7A4.15 13 PLIP interactions: 8 interactions with chain D, 5 interactions with chain B Hydrophobic interactions: D:V.47, D:F.221, D:F.221, D:I.229, D:I.229, D:F.232, B:D.55, B:L.58, B:R.84, B:W.87 pi-Stacking: D:F.221, D:F.221 Hydrogen bonds: B:W.87 7A4.14: 15 residues within 4Å: Chain B: V.47, L.218, F.221, K.222, I.229, L.233 Chain D: A.54, Q.57, L.58, L.61, L.83, R.84, W.87, L.91 Ligands: 7A4.15 11 PLIP interactions: 3 interactions with chain B, 8 interactions with chain D Hydrophobic interactions: B:V.47, B:F.221, D:A.54, D:Q.57, D:L.58, D:L.91 Salt bridges: B:K.222 Hydrogen bonds: D:W.87 pi-Stacking: D:W.87, D:W.87, D:W.87 7A4.15: 17 residues within 4Å: Chain D: 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: 7A4.9, GOL.10, 7A4.14 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:I.50, D:A.54, D:F.95, D:L.108, D:L.108, D:A.109, D:F.220, D:F.220, D:F.221 Hydrogen bonds: D:Q.57, D:A.109 Salt bridges: D:R.98

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

ACT.4: 4 residues within 4Å: Chain A: W.64, R.67, I.68 Ligands: DMS.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.68 Salt bridges: A:R.67 ACT.5: 3 residues within 4Å: Chain A: P.69, H.70, K.177 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.70, A:K.177 ACT.7: 9 residues within 4Å: Chain A: P.160, E.172, R.175, E.176, Y.179 Chain B: K.138, K.199, L.202, R.203 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:E.172, A:R.175 Salt bridges: A:R.175, B:K.138, B:R.203 Water bridges: B:K.138, B:K.199, B:R.203, B:R.203 ACT.8: 8 residues within 4Å: Chain A: A.122, K.222, L.223, I.224, G.225, D.226, T.227, P.228 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.226 Hydrogen bonds: A:D.226, A:T.227 ACT.11: 5 residues within 4Å: Chain B: R.16, K.66, R.67 Chain D: H.241, Q.242 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Salt bridges: B:R.16, B:R.67 Hydrophobic interactions: D:Q.242 ACT.12: 7 residues within 4Å: Chain B: Q.57, L.91, S.94, F.95, R.98, L.108, A.109 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.95 Hydrogen bonds: B:Q.57, B:A.109 Salt bridges: B:R.98 ACT.16: 6 residues within 4Å: Chain D: D.141, M.142, Q.143, Y.190, Q.193, R.196 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:Y.190 Hydrogen bonds: D:Q.143, D:Q.193 Salt bridges: D:R.196

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

DMS.6: 6 residues within 4Å: Chain A: I.68, P.69, C.151, V.178, S.181 Ligands: ACT.4 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 8 residues within 4Å: Chain B: I.50, C.51, A.54, W.87, L.218, F.221 Ligands: 7A4.9, 7A4.15 No protein-ligand interaction detected (PLIP) GOL.13: 8 residues within 4Å: Chain C: I.50, A.54, W.87, L.218, F.220, F.221 Ligands: 7A4.2, 7A4.3 No protein-ligand interaction detected (PLIP)

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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Retinoic acid receptor RXR-alpha

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