Research workbench
Group I intron-encoded homing endonuclease I-ceui complexed with DNA
Analyse Group I intron-encoded homing endonuclease I-ceui complexed with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EX5
- Type
- protein + DNA
- Length
- 466 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- I-ceui DNA target site; I-ceui DNA target site, complementary strand; DNA endonuclease…
- EC
- 3.1.-.-
- UniProt
- P32761
- Ligands
- CA
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 57% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | I-ceui DNA target site | dna | 26 | — | — |
| Y | I-ceui DNA target site, complementary strand | dna | 26 | — | — |
| A, B | DNA endonuclease I-ceui (EC 3.1.-.-) | protein | 207 | 57% helix, 15% strand | P32761 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains X, Y, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 170 | 0.77 | 0.93 | 32 | CA |
| 2 | 197 | 0.74 | 0.91 | 29 | empty |
| 3 | 179 | 0.69 | 0.88 | 32 | empty |
| 4 | 100 | 0.68 | 0.92 | 23 | empty |
| 5 | 124 | 0.63 | 0.87 | 24 | empty |
Interfaces
6 interfaces between chains.
- X–Y · 1265 Ų buried · 128 hydrogen bonds · nucleic-nucleic
- A–B · 1219 Ų buried · 8 hydrogen bonds · protein-protein
- Y–A · 1011 Ų buried · 23 hydrogen bonds · protein-nucleic
- Y–B · 981 Ų buried · 12 hydrogen bonds · protein-nucleic
- X–B · 951 Ų buried · 19 hydrogen bonds · protein-nucleic
Compared structures
- 2EX5 · Group I Intron-encoded Homing Endonuclease I-CeuI Complexed With DNA · the same entry in another collection · chain X against X, TM-score 1.00
- P32761 · AlphaFold monomer V2.0 prediction for DNA endonuclease I-ceui (P32761) · a predicted model of the same protein · chain B 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 P32761
- Elsewhere: RCSB PDB 2EX5 · PDBe 2EX5 · UniProt P32761
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