Research workbench
Crystal structure of full-length human DCAF15-DDB1-deltapbp-DDA1-RBM39 in complex with 4-(aminomethyl)-N-(3-cyano-4-methyl-1H-indol-7-yl) benzenesulfonamide
Analyse Crystal structure of full-length human DCAF15-DDB1-deltapbp-DDA1-RBM39 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UE5
- Type
- protein
- Length
- 1,377 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DDB1- and CUL4-associated factor 15; DNA damage-binding protein 1,DNA damage-binding…
- UniProt
- Q66K64, Q16531, Q7Z3L0, Q9BW61
- Ligands
- Q5J
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DDB1- and CUL4-associated factor 15 | protein | 424 | 11% helix, 39% strand | Q66K64 |
| B | DNA damage-binding protein 1,DNA damage-binding protein 1 | protein | 799 | 6% helix, 53% strand | Q16531 |
| C | RBM39 | protein | 81 | 27% helix, 38% strand | Q7Z3L0 |
| D | DET1- and DDB1-associated protein 1 | protein | 73 | 23% helix, 10% strand | Q9BW61 |
Ligands and binding sites
- Q5J · 4-(aminomethyl)-N-(3-cyano-4-methyl-1H-indol-7-yl) benzene-1-sulfonamide · ligand · chains A, C
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 598 | 0.84 | 0.89 | 73 | empty |
| 2 | 771 | 0.83 | 0.86 | 95 | Q5J |
| 3 | 720 | 0.80 | 0.84 | 72 | empty |
| 4 | 541 | 0.75 | 0.83 | 50 | empty |
| 5 | 436 | 0.75 | 0.84 | 57 | empty |
Interfaces
4 interfaces between chains.
- B–D · 3072 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 2376 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 1299 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 711 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6UE5 · Crystal structure of full-length human DCAF15-DDB1-deltaPBP-DDA1-RBM39 in complex with… · 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 0.98
- 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 0.29
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 6UE5 · PDBe 6UE5 · UniProt Q66K64 · UniProt Q16531 · UniProt Q7Z3L0 · UniProt Q9BW61
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