MolNFT v1 · #9662 · protein + DNA
Crystal structure of the DNA-binding domain of intron endonuclease I-tevi with its substrate
1I3J · 5'- D(*TP*TP*CP*TP*TP*GP*GP*GP*TP*CP*TP*AP*CP*CP*GP*TP*TP*TP…: “Crystal structure of the DNA-binding domain of intron endonuclease I-tevi with its substrate”. X-ray diffraction, 1 ligand (ZN), 1 pocket (best druggability 0.28).…
- PDB
- 1I3J
- Type
- protein + DNA
- Length
- 138 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'- D(*TP*TP*CP*TP*TP*GP*GP*GP*TP*CP*TP*AP*CP*CP*GP*TP*TP*TP*AP *AP*T)-3'; 5'…
- EC
- 3.1.-.-
- UniProt
- P13299
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.28
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'- D(*TP*TP*CP*TP*TP*GP*GP*GP*TP*CP*TP*AP*CP*CP*GP*TP*TP*TP*AP *AP*T)-3' | dna | 21 | — | — |
| C | 5'- D(*AP*AP*TP*TP*AP*AP*AP*CP*GP*GP*TP*AP*GP*AP*CP*CP*CP*AP*AP *GP*A)-3' | dna | 21 | — | — |
| A | Intron-associated endonuclease 1 (EC 3.1.-.-) | protein | 96 | 32% helix, 11% strand | P13299 |
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
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 | 74 | 0.28 | 0.72 | 16 | empty |
Interfaces
3 interfaces between chains.
- B–A · 1178 Ų buried · 29 hydrogen bonds · protein-nucleic
- C–A · 1147 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–C · 878 Ų buried · 68 hydrogen bonds · nucleic-nucleic
Compared structures
- 1I3J · Crystal structure of the DNA-binding domain of intron endonuclease I-tevi with its… · the same entry in another collection · chain B against B, 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 P13299
- Elsewhere: RCSB PDB 1I3J · PDBe 1I3J · UniProt P13299
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