SMTL ID : 6lb4.1

Crystal structure of dimeric RXR-LBD complexed with NEt-3ME and TIF2 co-activator

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

hetero-2-2-mer

Ligands

2 x E8L: 6-[ethyl-[3-(2-methoxyethoxy)-4-propan-2-yl-phenyl]amino]pyridine-3-carboxylic acid(Non-covalent)

E8L.1: 18 residues within 4Å: Chain A: I.49, A.52, A.53, Q.56, N.87, L.90, I.91, F.94, R.97, I.105, L.107, A.108, V.123, F.127, C.213, H.216, L.217, F.220 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.49, A:A.52, A:L.90, A:I.91, A:F.94, A:H.216, A:L.217, A:F.220 Hydrogen bonds: A:A.108 Water bridges: A:F.94 Salt bridges: A:R.97 pi-Stacking: A:F.94 E8L.6: 18 residues within 4Å: Chain C: I.49, A.52, A.53, Q.56, N.87, L.90, I.91, F.94, R.97, I.105, L.107, A.108, V.123, F.127, C.213, H.216, L.217, F.220 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:I.49, C:A.52, C:L.90, C:I.91, C:F.94, C:H.216, C:L.217, C:F.220 Hydrogen bonds: C:A.108 Water bridges: C:F.94 Salt bridges: C:R.97 pi-Stacking: C:F.94

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 5 residues within 4Å: Chain A: R.115, F.127, D.128, L.131, T.132 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.115, A:D.128, A:D.128 Water bridges: A:K.102 EDO.3: 5 residues within 4Å: Chain A: V.101, K.102, D.103, G.104, H.112 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.102, A:D.103, A:H.112 EDO.4: 6 residues within 4Å: Chain A: P.159, E.171, R.174, E.175, Y.178 Chain C: K.198 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Water bridges: C:G.194, A:E.175 EDO.5: 4 residues within 4Å: Chain A: R.129, S.208 Chain C: R.207, L.211 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:R.129, A:R.129, A:S.208, C:R.207 Water bridges: C:R.207 EDO.7: 5 residues within 4Å: Chain C: R.115, F.127, D.128, L.131, T.132 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.115, C:D.128 Water bridges: C:K.102 EDO.8: 5 residues within 4Å: Chain C: V.101, K.102, D.103, G.104, H.112 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.102, C:D.103, C:H.112 EDO.9: 6 residues within 4Å: Chain A: K.198 Chain C: P.159, E.171, R.174, E.175, Y.178 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain C Water bridges: A:G.194, C:E.175 Hydrogen bonds: C:E.171, C:E.175, C:Y.178 EDO.10: 4 residues within 4Å: Chain A: R.207, L.211 Chain C: R.129, S.208 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:R.129, C:R.129, C:S.208, A:R.207 Water bridges: A:R.207

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Imai, D. et al., Crystal structure of dimeric RXR-LBD complexed with NEt-3ME and TIF2 co-activator. To Be Published

Release Date

2020-11-18

Peptides

Retinoic acid receptor RXR-alpha: AC
Nuclear receptor coactivator 2: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Retinoic acid receptor RXR-alpha

Nuclear receptor coactivator 2

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