Research workbench
Structure of drosophila orc bound to at-rich DNA and CDC6
Analyse Structure of drosophila orc bound to at-rich DNA and CDC6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JK4
- Type
- protein + DNA
- Length
- 2,599 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Origin recognition complex subunit 2; Origin recognition complex subunit 3; Origin…
- UniProt
- Q24168, Q7K2L1, Q9W102, Q24169, Q9Y1B2, O16810, Q9VSM9
- Ligands
- ATP, MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 9 distinct chains · 55% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Origin recognition complex subunit 2 | protein | 290 | 49% helix, 12% strand | Q24168 |
| C | Origin recognition complex subunit 3 | protein | 612 | 61% helix, 8% strand | Q7K2L1 |
| D | Origin recognition complex subunit 4 | protein | 441 | 56% helix, 8% strand | Q9W102 |
| E | Origin recognition complex subunit 5 | protein | 398 | 52% helix, 9% strand | Q24169 |
| F | Origin recognition complex subunit 6 | protein | 17 | 76% helix, 0% strand | Q9Y1B2 |
| A | Origin recognition complex subunit 1 | protein | 401 | 51% helix, 11% strand | O16810 |
| G | Cell division control protein | protein | 372 | 56% helix, 11% strand | Q9VSM9 |
| H | DNA (34-mer) | dna | 34 | — | — |
| I | DNA (34-mer) | dna | 34 | — | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains D, E, C, A, G
- MG · Magnesium ion · metal · 4 copies · chains D, E, A, G
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 | 662 | 0.86 | 0.91 | 77 | ATP, MG |
| 2 | 626 | 0.81 | 0.86 | 78 | empty |
| 3 | 134 | 0.80 | 0.97 | 25 | empty |
| 4 | 723 | 0.78 | 0.83 | 65 | empty |
| 5 | 388 | 0.77 | 0.87 | 42 | ATP, MG |
Interfaces
27 interfaces between chains.
- D–A · 3840 Ų buried · 52 hydrogen bonds · protein-protein
- B–C · 3649 Ų buried · 32 hydrogen bonds · protein-protein
- D–E · 2867 Ų buried · 33 hydrogen bonds · protein-protein
- A–G · 2332 Ų buried · 20 hydrogen bonds · protein-protein
- C–E · 2130 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 7JK4 · Structure of Drosophila ORC bound to AT-rich DNA and Cdc6 · the same entry in another collection · chain I against I, TM-score 1.00
- O16810 · AlphaFold monomer V2.0 prediction for origin recognition complex subunit 1 (O16810) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q24169 · AlphaFold monomer V2.0 prediction for origin recognition complex subunit 5 (Q24169) · a predicted model of the same protein · chain E against A, TM-score 0.95
- Q9Y1B2 · AlphaFold monomer V2.0 prediction for origin recognition complex subunit 6 (Q9Y1B2) · a predicted model of the same protein · chain F against A, TM-score 0.85
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 Q24168
- Every structure of UniProt Q7K2L1
- Every structure of UniProt Q9W102
- Every structure of UniProt Q24169
- Every structure of UniProt Q9Y1B2
- Every structure of UniProt O16810
- Every structure of UniProt Q9VSM9
- Elsewhere: RCSB PDB 7JK4 · PDBe 7JK4 · UniProt Q24168 · UniProt Q7K2L1 · UniProt Q9W102 · UniProt Q24169 · UniProt Q9Y1B2 · UniProt O16810 · UniProt Q9VSM9
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