Research workbench
Crystal structure of the coiled-coil domain from listeria innocua phage integrase (tetragonal form II)
Analyse Crystal structure of the coiled-coil domain from listeria innocua phage… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UDO
- Type
- protein
- Length
- 374 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- A118 serine integrase
- UniProt
- Q928V6
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H | A118 serine integrase | protein | 48 | 65% helix, 0% strand | Q928V6 |
| B | A118 serine integrase | protein | 49 | 73% helix, 0% strand | Q928V6 |
| C | A118 serine integrase | protein | 44 | 77% helix, 0% strand | Q928V6 |
| D, F | A118 serine integrase | protein | 48 | 85% helix, 0% strand | Q928V6 |
| E | A118 serine integrase | protein | 47 | 70% helix, 0% strand | Q928V6 |
| G | A118 serine integrase | protein | 42 | 76% helix, 0% strand | Q928V6 |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 977 | 0.82 | 0.84 | 95 | empty |
| 2 | 144 | 0.44 | 0.75 | 18 | empty |
| 3 | 106 | 0.41 | 0.77 | 16 | empty |
| 4 | 83 | 0.35 | 0.75 | 16 | empty |
| 5 | 67 | 0.34 | 0.76 | 13 | empty |
Interfaces
15 interfaces between chains.
- G–H · 596 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 594 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 589 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 565 Ų buried · 7 hydrogen bonds · protein-protein
- E–H · 548 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5UDO · Crystal structure of the coiled-coil domain from Listeria Innocua Phage Integrase… · 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 Q928V6
- Elsewhere: RCSB PDB 5UDO · PDBe 5UDO · UniProt Q928V6
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