Research workbench
Testing the water-mediated hin recombinase DNA recognition by systematic mutations
Analyse Testing the water-mediated hin recombinase DNA recognition by systematic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JKR
- Type
- protein + DNA
- Length
- 74 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*TP*GP*TP*TP*TP*TP*TP*GP*AP*CP*AP*AP*GP*A)- 3'…
- UniProt
- P03013
- Pockets
- 1 · best druggability 0.31
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-D(*TP*GP*TP*TP*TP*TP*TP*GP*AP*CP*AP*AP*GP*A)- 3' | dna | 14 | — | — |
| B | 5'-D(*AP*TP*CP*TP*TP*GP*TP*CP*AP*AP*AP*AP*AP*C)- 3' | dna | 14 | — | — |
| C | DNA-invertase hin | protein | 46 | 54% helix, 0% strand | P03013 |
Ligands and binding sites
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B
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 | 62 | 0.31 | 0.75 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–B · 526 Ų buried · 52 hydrogen bonds · nucleic-nucleic
- A–C · 457 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–C · 407 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 1JKR · 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 0.93
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 1JKR · PDBe 1JKR · UniProt P03013
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