MolNFT v1 · #3646 · protein + DNA
Intron encoded homing endonuclease I-PPOI/DNA complex lacking catalytic metal ion
1CZ0 · DNA (5'- D(*TP*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*AP*GP*AP*GP*…: “Intron encoded homing endonuclease I-PPOI/DNA complex lacking catalytic metal ion”. X-ray diffraction, 2 ligands (ZN, NA), 6 pockets (best druggability 0.64). MolNFT v1…
- PDB
- 1CZ0
- Type
- protein + DNA
- Length
- 366 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*TP*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*AP*GP*AP*GP*AP*GP*TP *CP*A)-3')…
- EC
- 3.1.-.-
- UniProt
- Q94702
- Ligands
- ZN, NA
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | DNA (5'- D(*TP*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*AP*GP*AP*GP*AP*GP*TP *CP*A)-3') | dna | 21 | — | — |
| A, B | Intron-encoded homing endonuclease I-ppoi (EC 3.1.-.-) | protein | 162 | 19% helix, 33% strand | Q94702 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains C, B, D, 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 | 106 | 0.64 | 0.89 | 31 | empty |
| 2 | 222 | 0.51 | 0.76 | 35 | empty |
| 3 | 191 | 0.48 | 0.76 | 26 | empty |
| 4 | 77 | 0.31 | 0.74 | 15 | empty |
| 5 | 78 | 0.30 | 0.73 | 13 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2552 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 925 Ų buried · 69 hydrogen bonds · nucleic-nucleic
- C–A · 603 Ų buried · 5 hydrogen bonds · protein-nucleic
- D–B · 595 Ų buried · 6 hydrogen bonds · protein-nucleic
- D–A · 591 Ų buried · 17 hydrogen bonds · protein-nucleic
Compared structures
- 1CZ0 · Intron encoded homing endonuclease I-PPOI/DNA complex lacking catalytic metal ion · the same entry in another collection · chain C against C, TM-score 1.00
- Q94702 · AlphaFold monomer V2.0 prediction for intron-encoded endonuclease I-ppoi (Q94702) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q94702
- Elsewhere: RCSB PDB 1CZ0 · PDBe 1CZ0 · UniProt Q94702
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