MolNFT v1 · #25793 · protein
Structure of the aeropyrum pernix ORC2 protein (ADP form)
1W5S · Origin recognition complex subunit 2 ORC2: “Structure of the aeropyrum pernix ORC2 protein (ADP form)”. X-ray diffraction, 2 ligands (ADP, SO4), 7 pockets (best druggability 0.77). MolNFT v1 #25793 on GenesisL1: 3D structure…
- PDB
- 1W5S
- Type
- protein
- Length
- 786 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Origin recognition complex subunit 2 ORC2
- UniProt
- Q9YFU8
- Ligands
- ADP, SO4
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Origin recognition complex subunit 2 ORC2 | protein | 390 | 54% helix, 12% strand | Q9YFU8 |
| B | Origin recognition complex subunit 2 ORC2 | protein | 396 | 55% helix, 12% strand | Q9YFU8 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 566 | 0.77 | 0.84 | 48 | SO4 |
| 2 | 448 | 0.73 | 0.83 | 61 | ADP |
| 3 | 230 | 0.70 | 0.86 | 44 | ADP |
| 4 | 413 | 0.63 | 0.78 | 51 | SO4 |
| 5 | 124 | 0.40 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1566 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 1W5S · Structure of the Aeropyrum Pernix ORC2 protein (ADP form) · the same entry in another collection · chain A against A, TM-score 1.00
- Q9YFU8 · AlphaFold monomer V2.0 prediction for ORC1-type DNA replication protein 2 (Q9YFU8) · a predicted model of the same protein · chain B against A, TM-score 0.81
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 Q9YFU8
- Elsewhere: RCSB PDB 1W5S · PDBe 1W5S · UniProt Q9YFU8
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