MolNFT v1 · #163969 · protein
Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to RBM39 and indisulam
6SJ7 · DDB1- and CUL4-associated factor 15: “Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to RBM39 and indisulam”. Electron microscopy, 1 ligand (EF6), 20 pockets (best druggability 0.82). MolNFT v1 #163969 on…
- PDB
- 6SJ7
- Type
- protein
- Length
- 1,260 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DDB1- and CUL4-associated factor 15; DNA damage-binding protein 1; RNA binding protein…
- UniProt
- Q66K64, Q16531, Q7Z3L0, Q9BW61
- Ligands
- EF6
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 4 distinct chains · 9% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DDB1- and CUL4-associated factor 15 | protein | 355 | 10% helix, 36% strand | Q66K64 |
| B | DNA damage-binding protein 1 | protein | 774 | 7% helix, 48% strand | Q16531 |
| C | RNA binding protein 39 | protein | 79 | 24% helix, 29% strand | Q7Z3L0 |
| D | DET1- and DDB1-associated protein 1 | protein | 52 | 19% helix, 10% strand | Q9BW61 |
Ligands and binding sites
- EF6 · N~1~-(3-chloro-1H-indol-7-yl)benzene-1,4-disulfonamide · ligand · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 560 | 0.82 | 0.88 | 77 | EF6 |
| 2 | 561 | 0.81 | 0.87 | 80 | empty |
| 3 | 712 | 0.81 | 0.85 | 74 | empty |
| 4 | 143 | 0.77 | 0.95 | 35 | empty |
| 5 | 392 | 0.76 | 0.85 | 45 | empty |
Interfaces
4 interfaces between chains.
- B–D · 2542 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 2404 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1250 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 618 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6SJ7 · Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to RBM39 and Indisulam · the same entry in another collection · chain A against A, TM-score 1.00
- Q16531 · AlphaFold monomer V2.0 prediction for DNA damage-binding protein 1 (Q16531) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q66K64 · AlphaFold monomer V2.0 prediction for DDB1- and CUL4-associated factor 15 (Q66K64) · a predicted model of the same protein · chain A against A, TM-score 0.97
- Q9BW61 · AlphaFold monomer V2.0 prediction for DET1- and DDB1-associated protein 1 (Q9BW61) · a predicted model of the same protein · chain D against A, TM-score 0.27
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 Q66K64
- Every structure of UniProt Q16531
- Every structure of UniProt Q7Z3L0
- Every structure of UniProt Q9BW61
- Elsewhere: RCSB PDB 6SJ7 · PDBe 6SJ7 · UniProt Q66K64 · UniProt Q16531 · UniProt Q7Z3L0 · UniProt Q9BW61
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