Research workbench
Structural basis for catalytic activation of a serine recombinase
Analyse Structural basis for catalytic activation of a serine recombinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PKZ
- Type
- protein
- Length
- 1,486 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Recombinase sin
- UniProt
- D2J612
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, H, I, J, K, L | Recombinase sin | protein | 124 | 49% helix, 17% strand | D2J612 |
| G | Recombinase sin | protein | 122 | 48% helix, 17% strand | D2J612 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 20 copies · chains A, B, C, D, E, G, F, H, I, K, J, L
- EDO · 1,2-ethanediol · additive · 2 copies · chains H, I
- GOL · Glycerol · additive · 2 copies · chains I, K
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 | 429 | 0.69 | 0.80 | 46 | SO4 |
| 2 | 304 | 0.65 | 0.81 | 28 | SO4 |
| 3 | 324 | 0.63 | 0.79 | 34 | SO4 |
| 4 | 208 | 0.61 | 0.82 | 20 | empty |
| 5 | 221 | 0.61 | 0.81 | 26 | empty |
Interfaces
18 interfaces between chains.
- A–C · 750 Ų buried · 8 hydrogen bonds · protein-protein
- E–G · 750 Ų buried · 10 hydrogen bonds · protein-protein
- I–K · 736 Ų buried · 8 hydrogen bonds · protein-protein
- F–H · 697 Ų buried · 4 hydrogen bonds · protein-protein
- J–L · 686 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3PKZ · Structural basis for catalytic activation of a serine recombinase · 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 D2J612
- Elsewhere: RCSB PDB 3PKZ · PDBe 3PKZ · UniProt D2J612
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