MolNFT v1 · #140516 · protein

Crystal structure of pg-bound NURR1-lbd

5YD6 · Nuclear receptor subfamily 4 group a member 2: “Crystal structure of pg-bound NURR1-lbd”. X-ray diffraction, 2 ligands (8SU, MG), 13 pockets (best druggability 0.68). MolNFT v1 #140516 on GenesisL1: 3D structure, binding sites and…

PDB: 5YD6
Type: protein
Length: 901 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nuclear receptor subfamily 4 group a member 2
UniProt: P43354
Ligands: 8SU, MG
Pockets: 13 · best druggability 0.68

Structure

x-ray diffraction · 3 distinct chains · 68% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nuclear receptor subfamily 4 group a member 2	protein	224	70% helix, 4% strand	P43354
B	Nuclear receptor subfamily 4 group a member 2	protein	225	68% helix, 4% strand	P43354
C, D	Nuclear receptor subfamily 4 group a member 2	protein	226	66% helix, 4% strand	P43354

Ligands and binding sites

8SU · (~{Z})-7-[(1~{R},5~{S})-2-oxidanylidene-5-[(~{E}, 3~{S})-3-oxidanyloct-1-enyl]cyclopent-3-en-1-yl]hept-5-enoic acid · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	491	0.68	0.79	59	empty
2	428	0.68	0.80	53	empty
3	331	0.62	0.78	48	empty
4	117	0.61	0.86	22	8SU
5	125	0.61	0.85	25	8SU

Interfaces

4 interfaces between chains.

B–D · 891 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 827 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 300 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 60 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

5YD6 · Crystal structure of PG-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 0.98

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 5YD6 · PDBe 5YD6 · UniProt P43354

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