Research workbench
Crystal structure of reca superfamily ATPase PH0284 from pyrococcus horikoshii OT3
Analyse Crystal structure of reca superfamily ATPase PH0284 from pyrococcus horikoshii… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DR3
- Type
- protein
- Length
- 1,419 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UPF0273 protein PH0284
- UniProt
- O58022
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 32% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | UPF0273 protein PH0284 | protein | 232 | 31% helix, 28% strand | O58022 |
| B | UPF0273 protein PH0284 | protein | 240 | 30% helix, 30% strand | O58022 |
| C | UPF0273 protein PH0284 | protein | 233 | 33% helix, 30% strand | O58022 |
| D | UPF0273 protein PH0284 | protein | 242 | 32% helix, 27% strand | O58022 |
| E | UPF0273 protein PH0284 | protein | 236 | 31% helix, 30% strand | O58022 |
| F | UPF0273 protein PH0284 | protein | 236 | 32% helix, 28% strand | O58022 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F
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 | 673 | 0.77 | 0.82 | 63 | ADP |
| 2 | 561 | 0.77 | 0.84 | 58 | ADP |
| 3 | 566 | 0.77 | 0.83 | 58 | ADP |
| 4 | 517 | 0.76 | 0.84 | 56 | ADP |
| 5 | 566 | 0.74 | 0.82 | 69 | ADP |
Interfaces
6 interfaces between chains.
- A–B · 1231 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1226 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 1187 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 1186 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1140 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 2DR3 · Crystal Structure of RecA superfamily ATPase PH0284 from Pyrococcus horikoshii OT3 · the same entry in another collection · chain F against F, TM-score 1.00
- O58022 · AlphaFold monomer V2.0 prediction for UPF0273 protein PH0284 (O58022) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O58022
- Elsewhere: RCSB PDB 2DR3 · PDBe 2DR3 · UniProt O58022
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.