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Structure of DDB1-crbn-pomalidomide complex bound to IKZF1(ZF2)
Analyse Structure of DDB1-crbn-pomalidomide complex bound to IKZF1(ZF2) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H0F
- Type
- protein
- Length
- 4,940 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA damage-binding protein 1,DNA damage-binding protein 1, DNA damage-binding protein…
- UniProt
- Q96SW2, Q13422
- Ligands
- Y70, ZN
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | DNA damage-binding protein 1,DNA damage-binding protein 1, DNA damage-binding protein 1,DNA damage-binding protein 1 | protein | 826 | 8% helix, 51% strand | — |
| B, E, H, K | Protein cereblon | protein | 374 | 28% helix, 33% strand | Q96SW2 |
| C, F, I, L | DNA-binding protein ikaros | protein | 32 | 38% helix, 13% strand | Q13422 |
| D | DNA damage-binding protein 1,DNA damage-binding protein 1, DNA damage-binding protein 1,DNA damage-binding protein 1 | protein | 821 | 8% helix, 50% strand | — |
| J | DNA damage-binding protein 1,DNA damage-binding protein 1, DNA damage-binding protein 1,DNA damage-binding protein 1 | protein | 843 | 8% helix, 49% strand | — |
Ligands and binding sites
- Y70 · S-Pomalidomide · ligand · 4 copies · chains B, C, E, F, H, I, K, L
- ZN · Zinc ion · metal · 8 copies · chains B, C, E, F, H, I, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1124 | 0.86 | 0.87 | 84 | empty |
| 2 | 1150 | 0.86 | 0.87 | 97 | empty |
| 3 | 951 | 0.84 | 0.85 | 96 | empty |
| 4 | 610 | 0.84 | 0.89 | 47 | empty |
| 5 | 1007 | 0.84 | 0.85 | 101 | empty |
Interfaces
21 interfaces between chains.
- G–H · 2662 Ų buried · 27 hydrogen bonds · protein-protein
- D–E · 2602 Ų buried · 26 hydrogen bonds · protein-protein
- J–K · 2514 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 2514 Ų buried · 24 hydrogen bonds · protein-protein
- D–G · 583 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6H0F · Structure of DDB1-CRBN-pomalidomide complex bound to IKZF1(ZF2) · the same entry in another collection · chain L against L, 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 Q96SW2
- Every structure of UniProt Q13422
- Elsewhere: RCSB PDB 6H0F · PDBe 6H0F · UniProt Q96SW2 · UniProt Q13422
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