MolNFT v1 · #146648 · protein + DNA
Sequence requirements of the listeria innocua prophage attp site
6DNW · Putative integrase [bacteriophage A118]: “Sequence requirements of the listeria innocua prophage attp site”. X-ray diffraction, 1 ligand (ZN), 6 pockets (best druggability 0.72). MolNFT v1 #146648 on GenesisL1: 3D structure, binding…
- PDB
- 6DNW
- Type
- protein + DNA
- Length
- 283 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative integrase [bacteriophage A118]; DNA (26-mer)
- UniProt
- Q928V6
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative integrase [bacteriophage A118] | protein | 231 | 39% helix, 24% strand | Q928V6 |
| B | DNA (26-mer) | dna | 26 | — | — |
| C | DNA (26-mer) | dna | 26 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.72 | 0.98 | 19 | empty |
| 2 | 296 | 0.59 | 0.78 | 36 | empty |
| 3 | 107 | 0.41 | 0.77 | 16 | empty |
| 4 | 53 | 0.40 | 0.82 | 14 | empty |
| 5 | 101 | 0.35 | 0.74 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1551 Ų buried · 30 hydrogen bonds · protein-nucleic
- A–C · 1420 Ų buried · 28 hydrogen bonds · protein-nucleic
- B–C · 1128 Ų buried · 108 hydrogen bonds · nucleic-nucleic
Compared structures
- 6DNW · Sequence Requirements of the Listeria innocua prophage attP site · 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 6DNW · PDBe 6DNW · UniProt Q928V6
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