MolNFT v1 · #25794 · protein
Structure of the aeropyrum pernix ORC2 protein (adpnp-ADP complexes)
1W5T: “Structure of the aeropyrum pernix ORC2 protein (adpnp-ADP complexes)”. X-ray diffraction, 3 ligands (ANP, ADP, MG), 12 pockets (best druggability 0.80). MolNFT v1 #25794 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1W5T
- Type
- protein
- Length
- 1,182 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ORC2
- UniProt
- Q9YFU8
- Ligands
- ANP, ADP, MG
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 55% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ORC2 | protein | 394 | 56% helix, 13% strand | Q9YFU8 |
| B | ORC2 | protein | 396 | 55% helix, 13% strand | Q9YFU8 |
| C | ORC2 | protein | 392 | 54% helix, 11% strand | Q9YFU8 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · chains C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 726 | 0.80 | 0.84 | 72 | empty |
| 2 | 706 | 0.78 | 0.83 | 78 | ANP, MG |
| 3 | 605 | 0.78 | 0.84 | 70 | ANP, MG |
| 4 | 556 | 0.73 | 0.81 | 64 | ADP, MG |
| 5 | 483 | 0.65 | 0.77 | 49 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1354 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 811 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1W5T · Structure of the Aeropyrum Pernix ORC2 protein (ADPNP-ADP complexes) · 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 0.77
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 1W5T · PDBe 1W5T · UniProt Q9YFU8
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