Research workbench
Crystal structure of the homing endonuclease I-cvui in complex with its target (SRO1.3) in the presence of 2 mm ca
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
- 5A72
- Type
- protein + DNA
- Length
- 363 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA endonuclease I-cvui; 24MER DNA, 5'-D(*DTP*CP*AP*GP*AP*AP*CP*GP*TP*CP*GP*TP*AP…
- EC
- 3.1.-.-
- UniProt
- P56347
- Ligands
- CA
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA endonuclease I-cvui (EC 3.1.-.-) | protein | 157 | 54% helix, 20% strand | P56347 |
| B | DNA endonuclease I-cvui (EC 3.1.-.-) | protein | 158 | 54% helix, 20% strand | P56347 |
| C, D | 24MER DNA, 5'-D(*DTP*CP*AP*GP*AP*AP*CP*GP*TP*CP*GP*TP*AP *DCP*GP*AP*CP*GP*TP*TP*CP*TP*GP*A)-3' | dna | 24 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.72 | 0.97 | 21 | empty |
| 2 | 66 | 0.69 | 0.96 | 21 | empty |
| 3 | 97 | 0.62 | 0.89 | 24 | empty |
| 4 | 63 | 0.41 | 0.81 | 20 | empty |
| 5 | 50 | 0.25 | 0.73 | 11 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1171 Ų buried · 109 hydrogen bonds · nucleic-nucleic
- B–C · 1024 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–D · 1012 Ų buried · 20 hydrogen bonds · protein-nucleic
- B–D · 856 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–C · 850 Ų buried · 18 hydrogen bonds · protein-nucleic
Compared structures
- 5A72 · Crystal structure of the homing endonuclease I-CvuI in complex with its target (Sro1.3)… · the same entry in another collection · chain A against A, 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 5A72 · PDBe 5A72 · UniProt P56347
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.