Research workbench
P2 Integrase catalytic domain in space group P21
Analyse P2 Integrase catalytic domain in space group P21 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DOR
- Type
- protein
- Length
- 638 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- Enterobacteria phage P2
- Molecule
- Integrase
- UniProt
- P36932
- Ligands
- ZN, PO4
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · resolution 2.5 · 4 distinct chains · 54% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrase | protein | 162 | 53% helix, 7% strand | P36932 |
| B | Integrase | protein | 161 | 53% helix, 7% strand | P36932 |
| C | Integrase | protein | 158 | 54% helix, 8% strand | P36932 |
| D | Integrase | protein | 157 | 55% helix, 8% strand | P36932 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 227 | 0.69 | 0.85 | 40 | empty |
| 2 | 358 | 0.58 | 0.76 | 36 | empty |
| 3 | 133 | 0.51 | 0.80 | 27 | empty |
| 4 | 96 | 0.35 | 0.74 | 17 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2082 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 2080 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 399 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 331 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5DOR · P2 integrase catalytic domain in space group P21 · the same entry in another collection · chain A against A, TM-score 1.00
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 P36932
- Elsewhere: RCSB PDB 5DOR · PDBe 5DOR · UniProt P36932
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