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Cereblon isoform 4 from magnetospirillum gryphiswaldense in complex with thalidomide, wash I structure

Analyse Cereblon isoform 4 from magnetospirillum gryphiswaldense in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5AMI
Type: protein
Length: 289 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cereblon isoform 4
UniProt: A4TVL0
Ligands: EF2, ZN
Pockets: 3 · best druggability 0.60

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Cereblon isoform 4	protein	104	6% helix, 52% strand	A4TVL0
C	Cereblon isoform 4	protein	81	7% helix, 52% strand	A4TVL0

Ligands and binding sites

EF2 · S-Thalidomide · ligand · 2 copies · chains A, B
ZN · Zinc ion · metal · 3 copies · chains A, B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	394	0.60	0.76	49	empty
2	111	0.47	0.79	21	empty
3	60	0.37	0.78	13	EF2

Interfaces

3 interfaces between chains.

A–B · 518 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 499 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 11 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5AMI · Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Thalidomide… · 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 A4TVL0
Elsewhere: RCSB PDB 5AMI · PDBe 5AMI · UniProt A4TVL0

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