MolNFT v1 · #146294 · protein

NURR1 covalently modified by a dopamine metabolite

6DDA · Nuclear receptor subfamily 4 group a member 2: “NURR1 covalently modified by a dopamine metabolite”. X-ray diffraction, 3 ligands (G7J, K, BR), 6 pockets (best druggability 0.66). MolNFT v1 #146294 on GenesisL1: 3D structure…

PDB: 6DDA
Type: protein
Length: 685 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nuclear receptor subfamily 4 group a member 2
UniProt: P43354
Ligands: G7J, K, BR
Pockets: 6 · best druggability 0.66

Structure

x-ray diffraction · 3 distinct chains · 69% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Nuclear receptor subfamily 4 group a member 2	protein	236	70% helix, 4% strand	P43354
A	Nuclear receptor subfamily 4 group a member 2	protein	224	68% helix, 4% strand	P43354
C	Nuclear receptor subfamily 4 group a member 2	protein	225	68% helix, 4% strand	P43354

Ligands and binding sites

G7J · 5-hydroxy-1,2-dihydro-6H-indol-6-one · ligand · 3 copies · chains B, A, C
K · Potassium ion · metal · 5 copies · chains B, A, C
BR · Bromide ion · ion · 7 copies · chains B, A, C

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	406	0.66	0.79	43	BR
2	455	0.66	0.78	55	K, BR
3	143	0.48	0.78	23	empty
4	91	0.38	0.76	19	G7J
5	85	0.35	0.75	14	G7J

Interfaces

2 interfaces between chains.

B–A · 699 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 87 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 covalent, 1 modified (covalent ligand, oxidation).

Compared structures

6DDA · Nurr1 Covalently Modified by a Dopamine Metabolite · the same entry in another collection · chain B against B, 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 A against A, TM-score 0.98

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 6DDA · PDBe 6DDA · UniProt P43354

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