Research workbench
Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to RBM39 and sulfonamide E7820
Analyse Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to RBM39 and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PAI
- Type
- protein
- Length
- 1,649 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA damage-binding protein 1; DDB1- and CUL4-associated factor 15; RNA-binding protein…
- UniProt
- Q16531, Q66K64, Q7Z3L0, Q9BW61
- Ligands
- O6M, ZN
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA damage-binding protein 1 | protein | 1099 | 6% helix, 54% strand | Q16531 |
| C | DDB1- and CUL4-associated factor 15 | protein | 401 | 14% helix, 41% strand | Q66K64 |
| D | RNA-binding protein 39 | protein | 80 | 28% helix, 41% strand | Q7Z3L0 |
| E | DET1- and DDB1-associated protein 1 | protein | 69 | 20% helix, 10% strand | Q9BW61 |
Ligands and binding sites
- O6M · 3-cyano-N-(3-cyano-4-methyl-1H-indol-7-yl)benzene-1-sulfonamide · ligand · chains C, D
- ZN · Zinc ion · metal · chains C
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1009 | 0.87 | 0.88 | 100 | empty |
| 2 | 535 | 0.80 | 0.87 | 66 | empty |
| 3 | 402 | 0.76 | 0.86 | 50 | EPE |
| 4 | 103 | 0.76 | 0.96 | 27 | empty |
| 5 | 853 | 0.75 | 0.79 | 59 | empty |
Interfaces
4 interfaces between chains.
- A–E · 3771 Ų buried · 69 hydrogen bonds · protein-protein
- A–C · 2522 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1045 Ų buried · 14 hydrogen bonds · protein-protein
- C–E · 684 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6PAI · Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to RBM39 and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q66K64 · AlphaFold monomer V2.0 prediction for DDB1- and CUL4-associated factor 15 (Q66K64) · a predicted model of the same protein · chain C against A, TM-score 0.99
- Q16531 · AlphaFold monomer V2.0 prediction for DNA damage-binding protein 1 (Q16531) · a predicted model of the same protein · chain A against A, TM-score 0.95
- Q9BW61 · AlphaFold monomer V2.0 prediction for DET1- and DDB1-associated protein 1 (Q9BW61) · a predicted model of the same protein · chain E against A, TM-score 0.32
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 Q16531
- Every structure of UniProt Q66K64
- Every structure of UniProt Q7Z3L0
- Every structure of UniProt Q9BW61
- Elsewhere: RCSB PDB 6PAI · PDBe 6PAI · UniProt Q16531 · UniProt Q66K64 · UniProt Q7Z3L0 · UniProt Q9BW61
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