Research workbench
Structure of drosophila orc bound to DNA
Analyse Structure of drosophila orc bound to DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JK5
- Type
- protein + DNA
- Length
- 2,067 residues
- Chains
- 8
- 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
- Ligands
- ATP, MG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 8 distinct chains · 56% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Origin recognition complex subunit 2 | protein | 175 | 45% helix, 14% strand | Q24168 |
| C | Origin recognition complex subunit 3 | protein | 590 | 62% helix, 6% strand | Q7K2L1 |
| D | Origin recognition complex subunit 4 | protein | 441 | 56% helix, 9% strand | Q9W102 |
| E | Origin recognition complex subunit 5 | protein | 393 | 53% helix, 9% strand | Q24169 |
| F | Origin recognition complex subunit 6 | protein | 14 | 79% helix, 0% strand | Q9Y1B2 |
| A | Origin recognition complex subunit 1 | protein | 390 | 53% helix, 9% strand | O16810 |
| H | DNA (32-mer) | dna | 32 | — | — |
| I | DNA (32-mer) | dna | 32 | — | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains D, E, C, A
- MG · Magnesium ion · metal · 3 copies · chains D, E, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 841 | 0.87 | 0.90 | 86 | ATP, MG |
| 2 | 946 | 0.84 | 0.85 | 127 | empty |
| 3 | 1054 | 0.83 | 0.84 | 107 | empty |
| 4 | 166 | 0.82 | 0.98 | 27 | empty |
| 5 | 841 | 0.76 | 0.80 | 84 | ATP, MG |
Interfaces
18 interfaces between chains.
- D–A · 3715 Ų buried · 46 hydrogen bonds · protein-protein
- D–E · 2965 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 2924 Ų buried · 31 hydrogen bonds · protein-protein
- C–E · 1872 Ų buried · 16 hydrogen bonds · protein-protein
- H–I · 1352 Ų buried · 104 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7JK5 · Structure of Drosophila ORC bound to DNA · 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 0.98
- Q24168 · AlphaFold monomer V2.0 prediction for origin recognition complex subunit 2 (Q24168) · a predicted model of the same protein · chain B against A, TM-score 0.98
- 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 0.96
- 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 0.55
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
- Elsewhere: RCSB PDB 7JK5 · PDBe 7JK5 · UniProt Q24168 · UniProt Q7K2L1 · UniProt Q9W102 · UniProt Q24169 · UniProt Q9Y1B2 · UniProt O16810
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