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Crystal structure of ligand-bound NURR1-lbd

Analyse Crystal structure of ligand-bound NURR1-lbd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5Y41
Type: protein
Length: 464 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nuclear receptor subfamily 4 group a member 2
UniProt: P43354
Ligands: RPG, MG, CL
Pockets: 6 · best druggability 0.62

Structure

x-ray diffraction · 2 distinct chains · 69% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nuclear receptor subfamily 4 group a member 2	protein	232	68% helix, 4% strand	P43354
B	Nuclear receptor subfamily 4 group a member 2	protein	232	69% helix, 4% strand	P43354

Ligands and binding sites

RPG · (13E,15S)-15-hydroxy-9-oxoprosta-10,13-dien-1-oic acid · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · chains A
CL · Chloride ion · ion · 2 copies · chains A, B
PGE · Triethylene glycol · additive · chains A, B
PEG · Di(hydroxyethyl)ether · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	343	0.62	0.78	35	empty
2	266	0.62	0.80	31	empty
3	104	0.62	0.88	24	PGE
4	146	0.57	0.82	25	RPG
5	108	0.53	0.82	19	RPG

Interfaces

1 interface between chains.

A–B · 1011 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

5Y41 · Crystal Structure of LIGAND-BOUND NURR1-LBD · the same entry in another collection · chain A against A, TM-score 1.00
P43354 · AlphaFold monomer V2.0 prediction for nuclear receptor subfamily 4 group a member 2… · a predicted model of the same protein · chain B against A, TM-score 0.96

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P43354
Elsewhere: RCSB PDB 5Y41 · PDBe 5Y41 · UniProt P43354

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