MolNFT v1 · #178736 · protein + DNA
Structure of drosophila orc bound to gc-rich DNA and CDC6
7JK3 · Origin recognition complex subunit 2: “Structure of drosophila orc bound to gc-rich DNA and CDC6”. Electron microscopy, 2 ligands (ATP, MG), 20 pockets (best druggability 0.88). MolNFT v1 #178736 on GenesisL1: 3D structure, binding…
- PDB
- 7JK3
- Type
- protein + DNA
- Length
- 2,594 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 0.88
Structure
electron microscopy · 9 distinct chains · 53% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Origin recognition complex subunit 2 | protein | 285 | 48% helix, 11% strand | Q24168 |
| C | Origin recognition complex subunit 3 | protein | 614 | 60% helix, 7% strand | Q7K2L1 |
| D | Origin recognition complex subunit 4 | protein | 441 | 54% helix, 8% strand | Q9W102 |
| E | Origin recognition complex subunit 5 | protein | 398 | 48% helix, 10% 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 | 54% helix, 10% strand | Q9VSM9 |
| H | DNA (33-mer) | dna | 33 | — | — |
| I | DNA (33-mer) | dna | 33 | — | — |
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 | 1023 | 0.88 | 0.89 | 100 | ATP, MG |
| 2 | 587 | 0.83 | 0.88 | 65 | empty |
| 3 | 1011 | 0.83 | 0.84 | 108 | empty |
| 4 | 934 | 0.79 | 0.82 | 68 | empty |
| 5 | 684 | 0.78 | 0.83 | 62 | empty |
Interfaces
25 interfaces between chains.
- D–A · 3810 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 3571 Ų buried · 27 hydrogen bonds · protein-protein
- D–E · 2783 Ų buried · 25 hydrogen bonds · protein-protein
- A–G · 2269 Ų buried · 16 hydrogen bonds · protein-protein
- C–E · 2094 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 7JK3 · Structure of Drosophila ORC bound to GC-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 0.98
- 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 0.95
- 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 0.78
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 7JK3 · PDBe 7JK3 · UniProt Q24168 · UniProt Q7K2L1 · UniProt Q9W102 · UniProt Q24169 · UniProt Q9Y1B2 · UniProt O16810 · UniProt Q9VSM9
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