MolNFT v1 · #11323 · protein + DNA
Testing the water-mediated hin recombinase DNA recognition by systematic mutations.
1JJ6 · 5'-D(*TP*GP*TP*(5IT) P*TP*TP*TP*GP*AP*TP*AP*AP*GP*A)-3': “Testing the water-mediated hin recombinase DNA recognition by systematic mutations.”. X-ray diffraction, 1 pocket (best druggability 0.30). MolNFT v1 #11323 on GenesisL1: 3D…
- PDB
- 1JJ6
- Type
- protein + DNA
- Length
- 75 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*TP*GP*TP*(5IT) P*TP*TP*TP*GP*AP*TP*AP*AP*GP*A)-3'…
- UniProt
- P03013
- Pockets
- 1 · best druggability 0.30
Structure
x-ray diffraction · 3 distinct chains · 64% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-D(*TP*GP*TP*(5IT) P*TP*TP*TP*GP*AP*TP*AP*AP*GP*A)-3' | dna | 14 | — | — |
| B | 5'-D(*AP*TP*CP*TP*TP*AP*TP*CP*AP*AP*AP*AP*AP*C)- 3' | dna | 14 | — | — |
| C | DNA-invertase hin | protein | 47 | 64% helix, 0% strand | P03013 |
Ligands and binding sites
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.30 | 0.74 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 518 Ų buried · 40 hydrogen bonds · nucleic-nucleic
- A–C · 455 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–C · 390 Ų buried · 8 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 1JJ6 · Testing the Water-Mediated Hin Recombinase DNA Recognition by Systematic Mutations. · the same entry in another collection · chain A against A, TM-score 1.00
- P03013 · AlphaFold monomer V2.0 prediction for DNA-invertase hin (P03013) · a predicted model of the same protein · chain C against A, TM-score 0.94
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 P03013
- Elsewhere: RCSB PDB 1JJ6 · PDBe 1JJ6 · UniProt P03013
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