Research workbench
Crystal structure of the homing endonuclease I-CvuI in complex with its target (Sro1.3) in the presence of 2 mM Mn
Analyse Crystal structure of the homing endonuclease I-CvuI in complex with its target… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A74
- Type
- protein + DNA
- Length
- 363 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- CHLORELLA VULGARIS; SYNTHETIC CONSTRUCT
- Molecule
- DNA endonuclease I-cvui; 14MER DNA, 5'-D(*TP*CP*AP*GP*AP*AP*CP*GP*TP*CP*GP*TP*AP*CP)-3'…
- EC
- 3.1.-.-
- UniProt
- P56347
- Ligands
- MN
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · resolution 2.5 · 4 distinct chains · 52% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA endonuclease I-cvui (EC 3.1.-.-) | protein | 157 | 52% helix, 20% strand | P56347 |
| B | DNA endonuclease I-cvui (EC 3.1.-.-) | protein | 158 | 53% helix, 20% strand | P56347 |
| C, D | 14MER DNA, 5'-D(*TP*CP*AP*GP*AP*AP*CP*GP*TP*CP*GP*TP*AP*CP)-3' | dna | 14 | — | — |
| E, F | 10MER DNA, 5'-D(*GP*AP*CP*GP*TP*TP*CP*TP*GP*AP)-3' | dna | 10 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 3 copies · chains A, B, D, E, C, F
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 | 65 | 0.70 | 0.97 | 22 | empty |
| 2 | 59 | 0.68 | 0.96 | 22 | empty |
| 3 | 54 | 0.48 | 0.86 | 17 | empty |
| 4 | 58 | 0.45 | 0.84 | 20 | empty |
| 5 | 61 | 0.43 | 0.82 | 21 | empty |
Interfaces
15 interfaces between chains.
- A–D · 1015 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–C · 997 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–B · 775 Ų buried · 7 hydrogen bonds · protein-protein
- B–F · 748 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–E · 738 Ų buried · 24 hydrogen bonds · protein-nucleic
Compared structures
- 5A74 · Crystal structure of the homing endonuclease I-cvui in complex with its target (SRO1.3)… · the same entry in another collection · chain F against F, TM-score 1.00
- P56347 · AlphaFold monomer V2.0 prediction for DNA endonuclease I-cvui (P56347) · a predicted model of the same protein · 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 P56347
- Elsewhere: RCSB PDB 5A74 · PDBe 5A74 · UniProt P56347
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