9Q2D
Cryo-EM structure of ternary complex Ikaros-ZF2:CC-885:CRBN:DDB1 (molecular glue degrader)
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A (A) | DNA-binding protein Ikaros | polymer | 87 | 9731.4 | 1 | UniProt (Q13422) Pfam (PF00096) | Homo sapiens (human) | Ikaros family zinc finger protein 1,Lymphoid transcription factor LyF-1 |
| 2 | B (B) | Protein cereblon | polymer | 467 | 53582.0 | 1 | UniProt (Q96SW2) Pfam (PF02190) Pfam (PF03226) | Homo sapiens (human) | |
| 3 | C (C) | DNA damage-binding protein 1 | polymer | 836 | 93347.1 | 1 | UniProt (Q16531) Pfam (PF10433) Pfam (PF03178) | Homo sapiens (human) | DDB p127 subunit,DNA damage-binding protein a,DDBa,Damage-specific DNA-binding protein 1,HBV X-associated protein 1,XAP-1,UV-damaged DNA-binding factor,UV-damaged DNA-binding protein 1,UV-DDB 1,XPE-binding factor,XPE-BF,Xeroderma pigmentosum group E-complementing protein,XPCe |
| 4 | D, E (A, B) | ZINC ION | non-polymer | 65.4 | 2 | Chemie (ZN) | |||
| 5 | F (B) | 1-(3-chloro-4-methylphenyl)-3-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)urea | non-polymer | 440.9 | 1 | Chemie (85C) |
Sequence modifications
A: 112 - 196 (UniProt: Q13422)
B: 1 - 442 (UniProt: Q96SW2)
C: 1 - 699 (UniProt: Q16531)
C: 706 - 1140 (UniProt: Q16531)
| PDB | External Database | Details |
|---|---|---|
| Gly 110 | - | expression tag |
| Ser 111 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Met -24 | - | expression tag |
| Ser -23 | - | expression tag |
| Tyr -22 | - | expression tag |
| Tyr -21 | - | expression tag |
| His -20 | - | expression tag |
| His -19 | - | expression tag |
| His -18 | - | expression tag |
| His -17 | - | expression tag |
| His -16 | - | expression tag |
| His -15 | - | expression tag |
| Asp -14 | - | expression tag |
| Tyr -13 | - | expression tag |
| Asp -12 | - | expression tag |
| Ile -11 | - | expression tag |
| Pro -10 | - | expression tag |
| Thr -9 | - | expression tag |
| Thr -8 | - | expression tag |
| Gly -7 | - | expression tag |
| Leu -6 | - | expression tag |
| Val -5 | - | expression tag |
| Pro -4 | - | expression tag |
| Arg -3 | - | expression tag |
| Gly -2 | - | expression tag |
| Ser -1 | - | expression tag |
| Met 0 | - | expression tag |
C: 706 - 1140 (UniProt: Q16531)
| PDB | External Database | Details |
|---|---|---|
| Gly 700 | - | linker |
| Asn 701 | - | linker |
| Gly 702 | - | linker |
| Asn 703 | - | linker |
| Ser 704 | - | linker |
| Gly 705 | - | linker |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 3 |
| Total formula weight | 156660.5 | |
| Non-Polymers* | Number of molecules | 3 |
| Total formula weight | 571.7 | |
| All* | Total formula weight | 157232.2 |
