Research workbench
Structure of the aeropyrum pernix ORC1 protein in complex with DNA
Analyse Structure of the aeropyrum pernix ORC1 protein in complex with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2V1U
- Type
- protein + DNA
- Length
- 426 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division control protein 6 homolog; 5'-D(*TP*CP*TP*CP*CP*AP*CP*AP*GP*GP…
- UniProt
- Q9YEV6
- Ligands
- ADP, MG
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell division control protein 6 homolog | protein | 382 | 52% helix, 12% strand | Q9YEV6 |
| B | 5'-D(*TP*CP*TP*CP*CP*AP*CP*AP*GP*GP *AP*AP*AP*CP*GP*GP*AP*GP*GP*GP*GP*T)-3' | dna | 22 | — | — |
| C | 5'-D(*AP*CP*CP*CP*CP*TP*CP*CP*GP*TP *TP*TP*CP*CP*TP*GP*TP*GP*GP*AP*GP*A)-3' | dna | 22 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 357 | 0.70 | 0.83 | 38 | ADP, MG |
| 2 | 605 | 0.63 | 0.75 | 41 | empty |
| 3 | 83 | 0.42 | 0.79 | 15 | empty |
| 4 | 107 | 0.40 | 0.76 | 13 | empty |
Interfaces
3 interfaces between chains.
- B–C · 984 Ų buried · 99 hydrogen bonds · nucleic-nucleic
- A–C · 845 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–B · 828 Ų buried · 29 hydrogen bonds · protein-nucleic
Compared structures
- 2V1U · Structure of the aeropyrum pernix ORC1 protein in complex with DNA · the same entry in another collection · chain A against A, TM-score 1.00
- Q9YEV6 · AlphaFold monomer V2.0 prediction for ORC1-type DNA replication protein 1 (Q9YEV6) · a predicted model of the same protein · chain A against A, TM-score 0.87
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 Q9YEV6
- Elsewhere: RCSB PDB 2V1U · PDBe 2V1U · UniProt Q9YEV6
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