MolNFT v1 · #49038 · protein + DNA
Crystal structure of a heterodimer of CDC6/ORC1 initiators bound to origin DNA (from S. solfataricus)
2QBY · Cell division control protein 6 homolog 1: “Crystal structure of a heterodimer of CDC6/ORC1 initiators bound to origin DNA (from S. solfataricus)”. X-ray diffraction, 4 ligands (SPD, ADP, MG), 10 pockets (best druggability 0.72).…
- PDB
- 2QBY
- Type
- protein + DNA
- Length
- 800 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division control protein 6 homolog 1; Cell division control protein 6 homolog 3; DNA…
- UniProt
- Q980N4, Q97WM8
- Ligands
- SPD, ADP, MG, K
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell division control protein 6 homolog 1 | protein | 366 | 55% helix, 12% strand | Q980N4 |
| B | Cell division control protein 6 homolog 3 | protein | 368 | 53% helix, 11% strand | Q97WM8 |
| C | DNA (33-mer) | dna | 33 | — | — |
| D | DNA (33-mer) | dna | 33 | — | — |
Ligands and binding sites
- SPD · Spermidine · ligand · 2 copies · chains C, D
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- K · Potassium ion · metal · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 444 | 0.72 | 0.82 | 46 | MG, ADP |
| 2 | 131 | 0.67 | 0.88 | 31 | empty |
| 3 | 591 | 0.64 | 0.76 | 39 | empty |
| 4 | 284 | 0.61 | 0.80 | 37 | empty |
| 5 | 265 | 0.61 | 0.79 | 26 | MG, ADP |
Interfaces
6 interfaces between chains.
- C–D · 1391 Ų buried · 113 hydrogen bonds · nucleic-nucleic
- B–D · 759 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–D · 702 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–C · 696 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–C · 640 Ų buried · 16 hydrogen bonds · protein-nucleic
Compared structures
- 2QBY · Crystal structure of a heterodimer of Cdc6/Orc1 initiators bound to origin DNA (from S.… · the same entry in another collection · chain A against A, TM-score 1.00
- Q97WM8 · AlphaFold monomer V2.0 prediction for ORC1-type DNA replication protein 3 (Q97WM8) · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q980N4 · AlphaFold monomer V2.0 prediction for ORC1-type DNA replication protein 1 (Q980N4) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q980N4
- Every structure of UniProt Q97WM8
- Elsewhere: RCSB PDB 2QBY · PDBe 2QBY · UniProt Q980N4 · UniProt Q97WM8
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