Research workbench
Structure of DDB1-DDA1-DCAF15 complex bound to tasisulam and RBM39
Analyse Structure of DDB1-DDA1-DCAF15 complex bound to tasisulam and RBM39 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Q0V
- Type
- protein
- Length
- 1,313 residues
- Chains
- 5
- 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, Q14498, Q9BW61
- Ligands
- P7M, ZN
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 14% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA damage-binding protein 1 | protein | 772 | 9% helix, 54% strand | Q16531 |
| B | DDB1- and CUL4-associated factor 15 | protein | 208 | 15% helix, 39% strand | Q66K64 |
| C | DDB1- and CUL4-associated factor 15 | protein | 192 | 20% helix, 40% strand | Q66K64 |
| D | RNA-binding protein 39 | protein | 79 | 28% helix, 38% strand | Q14498 |
| E | DET1- and DDB1-associated protein 1 | protein | 62 | 35% helix, 8% strand | Q9BW61 |
Ligands and binding sites
- P7M · N-[(5-bromothiophen-2-yl)sulfonyl]-2,4-dichlorobenzamide · ligand · chains B, C, D
- ZN · Zinc ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1076 | 0.84 | 0.85 | 125 | P7M |
| 2 | 1145 | 0.83 | 0.84 | 99 | empty |
| 3 | 95 | 0.76 | 0.97 | 26 | empty |
| 4 | 523 | 0.75 | 0.82 | 47 | empty |
| 5 | 327 | 0.74 | 0.86 | 40 | empty |
Interfaces
7 interfaces between chains.
- B–C · 3410 Ų buried · 56 hydrogen bonds · protein-protein
- A–E · 2764 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 1918 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 790 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 770 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6Q0V · Structure of DDB1-DDA1-DCAF15 complex bound to tasisulam and RBM39 · the same entry in another collection · chain E against E, 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 A 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 B against A, TM-score 0.99
- Q14498 · AlphaFold monomer V2.0 prediction for RNA-binding protein 39 (Q14498) · a predicted model of the same protein · chain D against A, TM-score 0.96
- 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 0.31
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 Q14498
- Every structure of UniProt Q9BW61
- Elsewhere: RCSB PDB 6Q0V · PDBe 6Q0V · UniProt Q16531 · UniProt Q66K64 · UniProt Q14498 · UniProt Q9BW61
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