MolNFT v1 · #164901 · protein
Structure of DDB1 bound to CR8-engaged CDK12-cyclink
6TD3 · DNA damage-binding protein 1,DNA damage-binding protein 1: “Structure of DDB1 bound to CR8-engaged CDK12-cyclink”. X-ray diffraction, 1 ligand (RC8), 20 pockets (best druggability 0.82). MolNFT v1 #164901 on GenesisL1: 3D structure…
- PDB
- 6TD3
- Type
- protein
- Length
- 4,222 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA damage-binding protein 1,DNA damage-binding protein 1; Cyclin-dependent kinase 12…
- EC
- 2.7.11.22, 2.7.11.23
- UniProt
- Q16531, Q9NYV4, O75909
- Ligands
- RC8
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 16% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA damage-binding protein 1,DNA damage-binding protein 1 | protein | 826 | 8% helix, 51% strand | Q16531 |
| B, E, H | Cyclin-dependent kinase 12 (EC 2.7.11.22, 2.7.11.23) | protein | 333 | 33% helix, 15% strand | Q9NYV4 |
| C, F, I | Cyclin-K | protein | 248 | 68% helix, 0% strand | O75909 |
| D | DNA damage-binding protein 1,DNA damage-binding protein 1 | protein | 827 | 8% helix, 51% strand | Q16531 |
| G | DNA damage-binding protein 1,DNA damage-binding protein 1 | protein | 826 | 8% helix, 52% strand | Q16531 |
Ligands and binding sites
- RC8 · (2R)-2-({9-(1-methylethyl)-6-[(4-pyridin-2-ylbenzyl) amino]-9H-purin-2-yl}amino)butan-1-ol · ligand · 3 copies · chains A, B, D, E, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 944 | 0.82 | 0.83 | 95 | empty |
| 2 | 498 | 0.81 | 0.88 | 54 | empty |
| 3 | 472 | 0.80 | 0.87 | 50 | empty |
| 4 | 614 | 0.77 | 0.83 | 57 | empty |
| 5 | 603 | 0.77 | 0.83 | 48 | empty |
Interfaces
10 interfaces between chains.
- G–H · 2329 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 2239 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 2226 Ų buried · 14 hydrogen bonds · protein-protein
- H–I · 1277 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1267 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (phosphorylation).
Compared structures
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 Q9NYV4
- Every structure of UniProt O75909
- Elsewhere: RCSB PDB 6TD3 · PDBe 6TD3 · UniProt Q16531 · UniProt Q9NYV4 · UniProt O75909
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