SMTL ID : 5y41.3 (2 other biounits)

Crystal Structure of LIGAND-BOUND NURR1-LBD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

2 x RPG: (13E,15S)-15-hydroxy-9-oxoprosta-10,13-dien-1-oic acid(Covalent)

RPG.1: 15 residues within 4Å: Chain A: E.113, S.114, F.116, L.117, E.118, R.236, C.239, T.240, L.243, I.246, I.261, L.264, F.265, T.268, P.270 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.117, A:R.236, A:L.243, A:I.246, A:I.261, A:T.268, A:P.270 Hydrogen bonds: A:F.116, A:L.117 Water bridges: A:S.114, A:A.115 RPG.6: 14 residues within 4Å: Chain B: E.113, S.114, F.116, L.117, R.188, H.189, R.236, C.239, T.240, L.243, I.246, L.264, T.268, P.270 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:F.116, B:L.243, B:L.243, B:I.246, B:L.264, B:T.268, B:P.270 Hydrogen bonds: B:F.116, B:L.117, B:H.189, B:R.236 Water bridges: B:R.188 Salt bridges: B:R.188

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.2: 12 residues within 4Å: Chain A: D.172, I.173, S.174, H.211, F.214, N.215 Chain B: I.38, S.39, V.42, S.174, H.211, F.214 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.172, A:I.173, A:S.174, B:S.174

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 3 residues within 4Å: Chain A: P.98, G.99, K.203 No protein-ligand interaction detected (PLIP)

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

CL.4: 5 residues within 4Å: Chain A: S.86, I.90, R.123, R.127, C.138 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain B: S.86, I.90, R.123, R.127, C.138 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 1 residues within 4Å: Chain A: F.271 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:F.271, H2O.2, H2O.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rajan, S. et al., PGE1 and PGA1 bind to Nurr1 and activate its transcriptional function. Nat.Chem.Biol. (2020)

Release Date

2018-12-26

Peptides

Nuclear receptor subfamily 4 group A member 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nuclear receptor subfamily 4 group A member 2

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