MolNFT v1 · #178739 · protein
Structure of drosophila orc in the active conformation
7JK6 · Origin recognition complex subunit 4: “Structure of drosophila orc in the active conformation”. Electron microscopy, 2 ligands (ATP, MG), 20 pockets (best druggability 0.86). MolNFT v1 #178739 on GenesisL1: 3D structure, binding…
- PDB
- 7JK6
- Type
- protein
- Length
- 1,887 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Origin recognition complex subunit 4; Origin recognition complex subunit 5; Origin…
- UniProt
- Q9W102, Q24169, O16810, Q24168, Q7K2L1, Q9Y1B2
- Ligands
- ATP, MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 6 distinct chains · 57% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Origin recognition complex subunit 4 | protein | 438 | 57% helix, 8% strand | Q9W102 |
| E | Origin recognition complex subunit 5 | protein | 374 | 53% helix, 9% strand | Q24169 |
| A | Origin recognition complex subunit 1 | protein | 373 | 52% helix, 11% strand | O16810 |
| B | Origin recognition complex subunit 2 | protein | 165 | 43% helix, 14% strand | Q24168 |
| C | Origin recognition complex subunit 3 | protein | 520 | 66% helix, 6% strand | Q7K2L1 |
| F | Origin recognition complex subunit 6 | protein | 17 | 76% helix, 0% strand | Q9Y1B2 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains D, E, 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1063 | 0.86 | 0.88 | 125 | ATP, MG |
| 2 | 134 | 0.79 | 0.96 | 26 | empty |
| 3 | 629 | 0.78 | 0.84 | 67 | empty |
| 4 | 219 | 0.77 | 0.91 | 41 | empty |
| 5 | 592 | 0.76 | 0.83 | 59 | ATP, MG |
Interfaces
8 interfaces between chains.
- D–A · 3455 Ų buried · 47 hydrogen bonds · protein-protein
- D–E · 2788 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 2490 Ų buried · 26 hydrogen bonds · protein-protein
- E–C · 1854 Ų buried · 14 hydrogen bonds · protein-protein
- E–A · 647 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 7JK6 · Structure of Drosophila ORC in the active conformation · the same entry in another collection · chain F against F, TM-score 1.00
- 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
- 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 0.94
- 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 0.72
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 Q9W102
- Every structure of UniProt Q24169
- Every structure of UniProt O16810
- Every structure of UniProt Q24168
- Every structure of UniProt Q7K2L1
- Every structure of UniProt Q9Y1B2
- Elsewhere: RCSB PDB 7JK6 · PDBe 7JK6 · UniProt Q9W102 · UniProt Q24169 · UniProt O16810 · UniProt Q24168 · UniProt Q7K2L1 · UniProt Q9Y1B2
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