MolNFT v1 · #161006 · protein
Structure of DDB1-DDA1-DCAF15 complex bound to E7820 and RBM39
6Q0R · DNA damage-binding protein 1: “Structure of DDB1-DDA1-DCAF15 complex bound to E7820 and RBM39”. X-ray diffraction, 3 ligands (OXM, O6M, ZN), 17 pockets (best druggability 0.81). MolNFT v1 #161006 on GenesisL1: 3D structure, binding…
- PDB
- 6Q0R
- Type
- protein
- Length
- 1,312 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
- OXM, O6M, ZN
- Pockets
- 17 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 13% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA damage-binding protein 1 | protein | 783 | 8% helix, 53% strand | Q16531 |
| B | DDB1- and CUL4-associated factor 15 | protein | 208 | 14% helix, 38% strand | Q66K64 |
| C | DDB1- and CUL4-associated factor 15 | protein | 183 | 22% helix, 42% strand | Q66K64 |
| D | RNA-binding protein 39 | protein | 82 | 27% helix, 40% strand | Q14498 |
| E | DET1- and DDB1-associated protein 1 | protein | 56 | 27% helix, 11% strand | Q9BW61 |
Ligands and binding sites
- OXM · Oxamic acid · ligand · chains B
- O6M · 3-cyano-N-(3-cyano-4-methyl-1H-indol-7-yl)benzene-1-sulfonamide · 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
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 750 | 0.81 | 0.85 | 82 | empty |
| 2 | 347 | 0.80 | 0.90 | 53 | O6M |
| 3 | 438 | 0.78 | 0.86 | 59 | empty |
| 4 | 470 | 0.76 | 0.84 | 57 | empty |
| 5 | 84 | 0.75 | 0.97 | 21 | OXM |
Interfaces
7 interfaces between chains.
- B–C · 3202 Ų buried · 54 hydrogen bonds · protein-protein
- A–E · 2717 Ų buried · 49 hydrogen bonds · protein-protein
- A–B · 1819 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 796 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 728 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6Q0R · Structure of DDB1-DDA1-DCAF15 complex bound to E7820 and RBM39 · the same entry in another collection · chain E against E, 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 B 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 0.99
- 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 0.95
- 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 0.31
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 6Q0R · PDBe 6Q0R · UniProt Q16531 · UniProt Q66K64 · UniProt Q14498 · UniProt Q9BW61
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