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Mouse cereblon thalidomide binding domain complexed with racemic thalidomide

Analyse Mouse cereblon thalidomide binding domain complexed with racemic thalidomide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5YIZ
Type: protein
Length: 1,505 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein cereblon
UniProt: Q8C7D2
Ligands: EF2, ZN, SO4
Pockets: 9 · best druggability 0.75

Structure

x-ray diffraction · 6 distinct chains · 6% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Protein cereblon	protein	97	6% helix, 47% strand	Q8C7D2
G	Protein cereblon	protein	97	6% helix, 46% strand	Q8C7D2
J, n	Protein cereblon	protein	91	7% helix, 51% strand	Q8C7D2
M, Y, e, k	Protein cereblon	protein	94	6% helix, 48% strand	Q8C7D2
P, S, V, b, h, q	Protein cereblon	protein	93	6% helix, 49% strand	Q8C7D2
t	Protein cereblon	protein	98	6% helix, 47% strand	Q8C7D2

Ligands and binding sites

EF2 · S-Thalidomide · ligand · 16 copies · chains A, D, G, Y, J, M, P, S, V, b, e, h, k, t, n, q
ZN · Zinc ion · metal · 16 copies · chains A, D, G, J, M, P, S, V, Y, b, e, h, k, n, q, t
SO4 · Sulfate ion · ion · 30 copies · chains A, D, G, J, M, P, S, V, Y, b, h, e, k, t, n, q

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

Pockets

9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	980	0.75	0.78	60	EF2
2	1091	0.74	0.77	74	EF2
3	161	0.51	0.78	38	SO4
4	106	0.47	0.80	25	SO4
5	101	0.39	0.75	17	empty

Interfaces

26 interfaces between chains.

D–G · 796 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 788 Å² buried · 13 hydrogen bonds · protein-protein
A–G · 762 Å² buried · 12 hydrogen bonds · protein-protein
V–Y · 680 Å² buried · 14 hydrogen bonds · protein-protein
e–h · 662 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

5YIZ · Mouse Cereblon thalidomide binding domain complexed with racemic thalidomide · the same entry in another collection · chain b against b, 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 Q8C7D2
Elsewhere: RCSB PDB 5YIZ · PDBe 5YIZ · UniProt Q8C7D2

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