SMTL ID : 4cn5.1

Crystal Structure of the Human Retinoid X Receptor DNA-Binding Domain Bound to the Human Nr1d1 Response Element

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.10, C.13, C.27, C.30 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.10, A:C.13, A:C.27, A:C.30 ZN.2: 4 residues within 4Å: Chain A: C.46, C.52, C.62, C.65 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.46, A:C.52, A:C.62, A:C.65 ZN.6: 4 residues within 4Å: Chain B: C.10, C.13, C.27, C.30 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.10, B:C.13, B:C.27, B:C.30 ZN.7: 4 residues within 4Å: Chain B: C.46, C.52, C.62, C.65 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.46, B:C.52, B:C.62, B:C.65

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

CL.3: 3 residues within 4Å: Chain A: Y.44, Y.64, Q.68 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: D.55, K.56, R.57 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: C.46, R.47, C.62 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain B: K.35, R.39 Chain C: T.12, T.13 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain A: Q.63 Chain D: C.9 Ligand excluded by PLIP

4 x K: POTASSIUM ION(Non-functional Binders)

K.8: 2 residues within 4Å: Chain C: T.13, C.14 No protein-ligand interaction detected (PLIP) K.9: 2 residues within 4Å: Chain C: T.6, C.7 No protein-ligand interaction detected (PLIP) K.10: 2 residues within 4Å: Chain C: A.8, G.9 No protein-ligand interaction detected (PLIP) K.12: 3 residues within 4Å: Chain D: T.10, G.11 Ligands: NO3.13 No protein-ligand interaction detected (PLIP)

1 x NO3: NITRATE ION(Non-functional Binders)

NO3.13: 7 residues within 4Å: Chain B: Q.81, R.84 Chain C: G.9, A.10 Chain D: T.10, G.11 Ligands: K.12 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.81, B:R.84 Water bridges: B:R.84, A:N.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Osz, J. et al., Structural Basis of Natural Promoter Recognition by the Retinoid X Nuclear Receptor. Sci.Rep. (2015)

Release Date

2015-02-18

Peptides

RETINOIC ACID RECEPTOR RXR-ALPHA: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

RETINOIC ACID RECEPTOR RXR-ALPHA

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