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Human nuclear receptor liver receptor homologue-1, lrh-1, bound to an E. COLI phospholipid and a fragment of tif-2

Analyse Human nuclear receptor liver receptor homologue-1, lrh-1, bound to an E. COLI… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4PLE
Type: protein
Length: 1,001 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nuclear receptor subfamily 5 group a member 2; Nuclear receptor coactivator 2
UniProt: O00482, Q15596
Ligands: CPS, EPH
Pockets: 13 · best druggability 0.84

Structure

x-ray diffraction · 5 distinct chains · 71% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G	Nuclear receptor subfamily 5 group a member 2	protein	241	72% helix, 2% strand	O00482
B	Nuclear receptor coactivator 2	protein	9	67% helix, 0% strand	Q15596
C	Nuclear receptor subfamily 5 group a member 2	protein	239	72% helix, 3% strand	O00482
D, F, H	Nuclear receptor coactivator 2	protein	10	60% helix, 0% strand	Q15596
E	Nuclear receptor subfamily 5 group a member 2	protein	241	71% helix, 2% strand	O00482

Ligands and binding sites

CPS · 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate · ligand · 12 copies · chains A, G, E, C
EPH · L-alpha-phosphatidyl-beta-oleoyl-gamma-palmitoyl-phosphatidylethanolamine · ligand · 4 copies · chains A, G, C, E

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

Pockets

13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	994	0.84	0.85	77	EPH, CPS
2	1114	0.83	0.84	101	EPH, CPS
3	549	0.83	0.88	43	EPH, CPS
4	556	0.82	0.87	46	EPH, CPS
5	121	0.66	0.88	22	empty

Interfaces

12 interfaces between chains.

C–D · 587 Å² buried · 5 hydrogen bonds · protein-protein
G–H · 563 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 553 Å² buried · 3 hydrogen bonds · protein-protein
E–F · 548 Å² buried · 0 hydrogen bonds · protein-protein
A–G · 448 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

4PLE · Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, Bound to an E. Coli… · the same entry in another collection · chain H against H, TM-score 1.00
O00482 · AlphaFold monomer V2.0 prediction for nuclear receptor subfamily 5 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 O00482
Every structure of UniProt Q15596
Elsewhere: RCSB PDB 4PLE · PDBe 4PLE · UniProt O00482 · UniProt Q15596

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