MolNFT v1 · #107082 · protein

Crystal structure of murine cereblon in complex with thalidomide

4TZC · Protein cereblon: “Crystal structure of murine cereblon in complex with thalidomide”. X-ray diffraction, 3 ligands (EF2, ZN, SO4), 2 pockets (best druggability 0.77). MolNFT v1 #107082 on GenesisL1: 3D structure, binding sites and…

PDB: 4TZC
Type: protein
Length: 391 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein cereblon
UniProt: Q8C7D2
Ligands: EF2, ZN, SO4
Pockets: 2 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 8% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Protein cereblon	protein	93	6% helix, 48% strand	Q8C7D2
A	Protein cereblon	protein	91	7% helix, 49% strand	Q8C7D2
B	Protein cereblon	protein	100	6% helix, 46% strand	Q8C7D2
D	Protein cereblon	protein	107	12% helix, 42% strand	Q8C7D2

Ligands and binding sites

EF2 · S-Thalidomide · ligand · 4 copies · chains C, A, B, D
ZN · Zinc ion · metal · 4 copies · chains C, A, B, D
SO4 · Sulfate ion · ion · 8 copies · chains C, A, B, D

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	825	0.77	0.80	72	EF2
2	362	0.56	0.74	51	empty

Interfaces

5 interfaces between chains.

C–A · 625 Å² buried · 14 hydrogen bonds · protein-protein
B–D · 529 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 187 Å² buried · 0 hydrogen bonds · protein-protein
A–B · 17 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 13 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4TZC · Crystal Structure of Murine Cereblon in Complex with Thalidomide · the same entry in another collection · chain D against D, TM-score 1.00
Q8C7D2 · AlphaFold monomer V2.0 prediction for protein cereblon (Q8C7D2) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 4TZC · PDBe 4TZC · UniProt Q8C7D2

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