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Crystal structure of raralpha ligand binding domain in complex with a fragment of the TIF2 coactivator

Analyse Crystal structure of raralpha ligand binding domain in complex with a fragment… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7APO
Type: protein
Length: 518 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Retinoic acid receptor alpha; Nuclear receptor coactivator 2
UniProt: P10276, E7EWM1
Ligands: EQN
Pockets: 9 · best druggability 0.80

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Retinoic acid receptor alpha	protein	233	67% helix, 4% strand	P10276
B	Retinoic acid receptor alpha	protein	233	70% helix, 4% strand	P10276
C, D	Nuclear receptor coactivator 2	protein	26	73% helix, 0% strand	E7EWM1

Ligands and binding sites

EQN · 4-{[(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)carbonyl]amino}benzoic acid · ligand · 2 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains B, C

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

Pockets

9 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	234	0.80	0.92	38	EQN
2	252	0.80	0.92	38	EQN
3	429	0.67	0.79	39	empty
4	428	0.66	0.78	37	empty
5	144	0.50	0.79	22	empty

Interfaces

3 interfaces between chains.

A–B · 1347 Å² buried · 15 hydrogen bonds · protein-protein
B–D · 679 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 677 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

7APO · Crystal structure of RARalpha ligand binding domain in complex with a fragment of the… · the same entry in another collection · chain A against A, TM-score 1.00
P10276 · AlphaFold monomer V2.0 prediction for retinoic acid receptor alpha (P10276) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P10276
Every structure of UniProt E7EWM1
Elsewhere: RCSB PDB 7APO · PDBe 7APO · UniProt P10276 · UniProt E7EWM1

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