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Crystal structure of NURR1 lbd

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

PDB: 1OVL
Type: protein
Length: 1,393 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Orphan nuclear receptor NURR1 (mse 414, 496, 511); Orphan nuclear receptor NURR1 (mse…
UniProt: P43354
Ligands: K, BR, IOD
Pockets: 12 · best druggability 0.80

Structure

x-ray diffraction · 6 distinct chains · 66% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Orphan nuclear receptor NURR1 (mse 414, 496, 511)	protein	228	66% helix, 4% strand	P43354
B	Orphan nuclear receptor NURR1 (mse 496, 511)	protein	236	68% helix, 4% strand	P43354
C	Orphan nuclear receptor NURR1 (mse 496, 511)	protein	226	66% helix, 4% strand	P43354
D	Orphan nuclear receptor NURR1 (mse 414, 496, 511)	protein	230	67% helix, 4% strand	P43354
E	Orphan nuclear receptor NURR1 (mse 496, 511)	protein	250	65% helix, 4% strand	P43354
F	Orphan nuclear receptor NURR1 (mse 496, 511)	protein	223	67% helix, 4% strand	P43354

Ligands and binding sites

K · Potassium ion · metal · 8 copies · chains A, B, D, E, F
BR · Bromide ion · ion · 19 copies · chains A, B, C, E, F, D
IOD · Iodide ion · ion · chains B, E

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1057	0.80	0.81	101	BR, K, IOD
2	757	0.75	0.80	68	BR
3	358	0.68	0.81	37	BR
4	395	0.68	0.80	42	BR
5	335	0.66	0.81	31	K, BR

Interfaces

10 interfaces between chains.

D–E · 937 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 827 Å² buried · 13 hydrogen bonds · protein-protein
C–F · 542 Å² buried · 0 hydrogen bonds · protein-protein
C–E · 350 Å² buried · 4 hydrogen bonds · protein-protein
B–E · 318 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 modified (engineered).

Compared structures

1OVL · Crystal Structure of Nurr1 LBD · the same entry in another collection · chain F against F, 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 C against A, TM-score 0.97

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 1OVL · PDBe 1OVL · UniProt P43354

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