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Crystal structure of rxr-alpha ligand binding domain complexed with synthetic modulator K8003

Analyse Crystal structure of rxr-alpha ligand binding domain complexed with synthetic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5TBP
Type: protein
Length: 822 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Retinoic acid receptor rxr-alpha
UniProt: P19793
Ligands: 7A4
Pockets: 9 · best druggability 0.87

Structure

x-ray diffraction · 3 distinct chains · 70% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Retinoic acid receptor rxr-alpha	protein	198	71% helix, 3% strand	P19793
B	Retinoic acid receptor rxr-alpha	protein	213	69% helix, 3% strand	P19793
C	Retinoic acid receptor rxr-alpha	protein	213	69% helix, 3% strand	P19793

Ligands and binding sites

7A4 · [(1Z)-5-fluoro-2-methyl-1-{[4-(propan-2-yl) phenyl]methylidene}-1H-inden-3-yl]acetic acid · ligand · 6 copies · chains A, C, B, D
ACT · Acetate ion · additive · 7 copies · chains A, B, D
GOL · Glycerol · additive · 2 copies · chains B, C
DMS · Dimethyl sulfoxide · additive · chains A

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

Pockets

9 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	992	0.87	0.87	93	7A4, GOL
2	856	0.85	0.87	71	7A4, GOL, ACT
3	158	0.67	0.87	30	empty
4	51	0.60	0.92	13	ACT
5	103	0.58	0.86	16	empty

Interfaces

5 interfaces between chains.

A–C · 1539 Å² buried · 17 hydrogen bonds · protein-protein
B–D · 1493 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 1232 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1216 Å² buried · 19 hydrogen bonds · protein-protein
A–D · 27 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

5TBP · Crystal Structure of RXR-alpha ligand binding domain complexed with synthetic modulator… · the same entry in another collection · chain A against A, TM-score 1.00

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 P19793
Elsewhere: RCSB PDB 5TBP · PDBe 5TBP · UniProt P19793

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