SMTL ID : 1h9u.1

The structure of the human retinoid-X-receptor beta ligand binding domain in complex with the specific synthetic agonist LG100268

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-octamer

Ligands

8 x LG2: 6-[1-(3,5,5,8,8-PENTAMETHYL-5,6,7,8-TETRAHYDRONAPHTHALEN-2-YL)CYCLOPROPYL]PYRIDINE-3-CARBOXYLIC ACID(Non-covalent)

LG2.1: 16 residues within 4Å: Chain A: I.41, A.44, A.45, Q.48, W.78, N.79, L.82, I.83, F.86, R.89, L.99, A.100, I.118, V.122, C.205, H.208 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.41, A:W.78, A:L.82, A:I.83, A:F.86, A:F.86, A:F.86, A:I.118, A:I.118, A:V.122, A:H.208 Hydrogen bonds: A:A.100 Water bridges: A:F.86 Salt bridges: A:R.89 pi-Stacking: A:F.86 LG2.4: 16 residues within 4Å: Chain B: I.41, A.44, A.45, Q.48, W.78, L.82, I.83, F.86, R.89, L.99, A.100, V.115, I.118, C.205, H.208, L.209 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:I.41, B:W.78, B:L.82, B:I.83, B:F.86, B:V.115, B:I.118, B:I.118, B:H.208, B:L.209 Hydrogen bonds: B:A.100 Water bridges: B:F.86 Salt bridges: B:R.89 pi-Stacking: B:F.86 LG2.7: 16 residues within 4Å: Chain C: V.38, I.41, A.44, A.45, Q.48, W.78, N.79, L.82, I.83, F.86, R.89, L.99, A.100, I.118, C.205, H.208 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:V.38, C:I.41, C:W.78, C:L.82, C:I.83, C:F.86, C:I.118, C:I.118, C:H.208 Hydrogen bonds: C:A.100 Water bridges: C:F.86 Salt bridges: C:R.89 pi-Stacking: C:F.86 LG2.9: 16 residues within 4Å: Chain D: I.41, A.44, A.45, Q.48, W.78, L.82, I.83, F.86, R.89, L.99, A.100, I.118, V.122, C.205, H.208, L.209 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:I.41, D:W.78, D:L.82, D:I.83, D:F.86, D:I.118, D:I.118, D:V.122, D:H.208, D:L.209 Hydrogen bonds: D:A.100 Water bridges: D:F.86 Salt bridges: D:R.89 LG2.11: 16 residues within 4Å: Chain E: I.41, A.44, A.45, Q.48, W.78, N.79, L.82, I.83, F.86, R.89, L.99, A.100, I.118, V.122, C.205, H.208 15 PLIP interactions: 15 interactions with chain E Hydrophobic interactions: E:I.41, E:W.78, E:L.82, E:I.83, E:F.86, E:F.86, E:F.86, E:I.118, E:I.118, E:V.122, E:H.208 Hydrogen bonds: E:A.100 Water bridges: E:F.86 Salt bridges: E:R.89 pi-Stacking: E:F.86 LG2.14: 16 residues within 4Å: Chain F: I.41, A.44, A.45, Q.48, W.78, L.82, I.83, F.86, R.89, L.99, A.100, V.115, I.118, C.205, H.208, L.209 14 PLIP interactions: 14 interactions with chain F Hydrophobic interactions: F:I.41, F:W.78, F:L.82, F:I.83, F:F.86, F:V.115, F:I.118, F:I.118, F:H.208, F:L.209 Hydrogen bonds: F:A.100 Water bridges: F:F.86 Salt bridges: F:R.89 pi-Stacking: F:F.86 LG2.17: 16 residues within 4Å: Chain G: V.38, I.41, A.44, A.45, Q.48, W.78, N.79, L.82, I.83, F.86, R.89, L.99, A.100, I.118, C.205, H.208 13 PLIP interactions: 13 interactions with chain G Hydrophobic interactions: G:V.38, G:I.41, G:W.78, G:L.82, G:I.83, G:F.86, G:I.118, G:I.118, G:H.208 Hydrogen bonds: G:A.100 Water bridges: G:F.86 Salt bridges: G:R.89 pi-Stacking: G:F.86 LG2.19: 16 residues within 4Å: Chain H: I.41, A.44, A.45, Q.48, W.78, L.82, I.83, F.86, R.89, L.99, A.100, I.118, V.122, C.205, H.208, L.209 13 PLIP interactions: 13 interactions with chain H Hydrophobic interactions: H:I.41, H:W.78, H:L.82, H:I.83, H:F.86, H:I.118, H:I.118, H:V.122, H:H.208, H:L.209 Hydrogen bonds: H:A.100 Water bridges: H:F.86 Salt bridges: H:R.89

8 x NI: NICKEL (II) ION(Non-covalent)

NI.2: 3 residues within 4Å: Chain A: H.104, H.106 Ligands: CL.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.104, A:H.106 NI.5: 3 residues within 4Å: Chain B: H.104, H.106 Ligands: CL.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.104, B:H.106 NI.8: 2 residues within 4Å: Chain C: H.104, H.106 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.104, C:H.106 NI.10: 2 residues within 4Å: Chain D: H.104, H.106 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:H.104, D:H.106 NI.12: 3 residues within 4Å: Chain E: H.104, H.106 Ligands: CL.13 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:H.104, E:H.106 NI.15: 3 residues within 4Å: Chain F: H.104, H.106 Ligands: CL.16 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:H.104, F:H.106 NI.18: 2 residues within 4Å: Chain G: H.104, H.106 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:H.104, G:H.106 NI.20: 2 residues within 4Å: Chain H: H.104, H.106 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:H.104, H:H.106

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 3 residues within 4Å: Chain A: H.104, H.106 Ligands: NI.2 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain B: H.104, H.106 Ligands: NI.5 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain E: H.104, H.106 Ligands: NI.12 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain F: H.104, H.106 Ligands: NI.15 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Love, J.D. et al., The Structural Basis for the Specificity of Retinoid-X Receptor-Selective Agonists: New Insights Into the Role of Helix H12. J.Biol.Chem. (2002)

Release Date

2002-04-03

Peptides

RETINOID X RECEPTOR, BETA: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

RETINOID X RECEPTOR, BETA