MolNFT v1 · #113167 · 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 cleaved
5A77 · 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), 4 pockets (best druggability 0.73). MolNFT v1 #113167 on…
- PDB
- 5A77
- Type
- protein + DNA
- Length
- 363 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA endonuclease I-cvui; 14MER DNA, 5'-D(*TP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*DCP)-3'…
- EC
- 3.1.-.-
- UniProt
- P56347
- Ligands
- MG
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 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 | 52% helix, 20% strand | P56347 |
| C, D | 14MER DNA, 5'-D(*TP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*DCP)-3' | dna | 14 | — | — |
| E, F | 10MER DNA, 5'-D(*GP*AP*CP*GP*TP*TP*TP*TP* GP*AP*DGP*AP*CP*GP*TP*TP*TP*TP*GP*A)-3' | dna | 10 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B, C, F, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.73 | 0.97 | 20 | empty |
| 2 | 65 | 0.69 | 0.96 | 20 | empty |
| 3 | 174 | 0.66 | 0.87 | 32 | empty |
| 4 | 56 | 0.43 | 0.83 | 19 | empty |
Interfaces
14 interfaces between chains.
- A–D · 896 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–C · 860 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–B · 835 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 740 Ų buried · 29 hydrogen bonds · protein-nucleic
- B–F · 719 Ų buried · 29 hydrogen bonds · protein-nucleic
Compared structures
- 5A77 · Crystal structure of the homing endonuclease I-CvuI in complex with I- CreI target… · 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 5A77 · PDBe 5A77 · UniProt P56347
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