MolNFT v1 · #113168 · protein + DNA
Crystal structure of the homing endonuclease I-cvui in complex with I-crei target (C1221) in the presence of 2 mm mg revealing DNA not cleaved
5A78 · DNA endonuclease I-cvui: “Crystal structure of the homing endonuclease I-cvui in complex with I-crei target (C1221) in the presence of…”. X-ray diffraction, 1 ligand (MG), 3 pockets (best druggability 0.75). MolNFT v1 #113168 on…
- PDB
- 5A78
- 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(*TP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP…
- EC
- 3.1.-.-
- UniProt
- P56347
- Ligands
- MG
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA endonuclease I-cvui (EC 3.1.-.-) | protein | 157 | 51% helix, 20% strand | P56347 |
| B | DNA endonuclease I-cvui (EC 3.1.-.-) | protein | 158 | 53% helix, 20% strand | P56347 |
| C, D | 24MER DNA, 5'-D(*TP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP *CP*GP*AP*CP*GP*TP*TP*TP*TP*GP*A)-3' | dna | 24 | — | — |
Ligands and binding sites
- MG · Magnesium 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
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.75 | 0.98 | 22 | empty |
| 2 | 64 | 0.72 | 0.98 | 18 | empty |
| 3 | 70 | 0.45 | 0.82 | 22 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1171 Ų buried · 99 hydrogen bonds · nucleic-nucleic
- B–C · 960 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–D · 949 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–C · 875 Ų buried · 25 hydrogen bonds · protein-nucleic
- B–D · 866 Ų buried · 29 hydrogen bonds · protein-nucleic
Compared structures
- 5A78 · Crystal structure of the homing endonuclease I-CvuI in complex with I- CreI target… · 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 5A78 · PDBe 5A78 · UniProt P56347
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