MolNFT v1 · #23546 · protein + DNA
DNA binding and cleavage by the hnh homing endonuclease I-hmui
1U3E · 36-mer: “DNA binding and cleavage by the hnh homing endonuclease I-hmui”. X-ray diffraction, 2 ligands (SR, MN), 4 pockets (best druggability 0.50). MolNFT v1 #23546 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1U3E
- Type
- protein + DNA
- Length
- 246 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 36-mer; 5'-D(*CP*TP*TP*AP*CP*GP*TP*GP*GP*GP*AP*AP*TP*TP*GP*CP*TP*GP *AP*GP*C)-3'…
- UniProt
- P34081
- Ligands
- SR, MN
- Pockets
- 4 · best druggability 0.50
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 36-mer | dna | 36 | — | — |
| B | 5'-D(*CP*TP*TP*AP*CP*GP*TP*GP*GP*GP*AP*AP*TP*TP*GP*CP*TP*GP *AP*GP*C)-3' | dna | 21 | — | — |
| C | 5'-D(P*GP*TP*TP*AP*GP*GP*CP*TP*CP*AP*TP*TP*AP*CP*T)-3' | dna | 15 | — | — |
| M | Hnh homing endonuclease | protein | 174 | 29% helix, 27% strand | P34081 |
Ligands and binding sites
- SR · Strontium ion · metal · 4 copies · chains A, M, B
- MN · Manganese (II) ion · metal · chains B, C, M
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, C, M
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.50 | 0.80 | 23 | EDO |
| 2 | 107 | 0.38 | 0.76 | 15 | empty |
| 3 | 79 | 0.31 | 0.74 | 15 | empty |
| 4 | 66 | 0.30 | 0.75 | 13 | SR |
Interfaces
6 interfaces between chains.
- A–M · 1532 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–B · 955 Ų buried · 68 hydrogen bonds · nucleic-nucleic
- B–M · 923 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–C · 753 Ų buried · 60 hydrogen bonds · nucleic-nucleic
- C–M · 518 Ų buried · 19 hydrogen bonds · protein-nucleic
Compared structures
- 1U3E · DNA binding and cleavage by the HNH homing endonuclease I-HmuI · 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 P34081
- Elsewhere: RCSB PDB 1U3E · PDBe 1U3E · UniProt P34081
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