Research workbench
L116A mutant of the homing endonuclease I-ppoi complexed to homing site DNA.
Analyse L116A mutant of the homing endonuclease I-ppoi complexed to homing site DNA. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EVW
- Type
- protein + DNA
- Length
- 728 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*TP*GP*GP*CP*TP*AP*CP*CP*TP*TP*AP*A)-3'); DNA…
- UniProt
- Q94702
- Ligands
- ZN, MG
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 19% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, G | DNA (5'-D(*TP*GP*GP*CP*TP*AP*CP*CP*TP*TP*AP*A)-3') | dna | 12 | — | — |
| M, N | DNA (5'-D(P*GP*AP*GP*AP*GP*TP*CP*A)-3') | dna | 8 | — | — |
| F, H | DNA (5'-D(*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*A)-3') | dna | 12 | — | — |
| O, P | DNA (5'-D(P*GP*GP*TP*AP*GP*CP*CP*A)-3') | dna | 8 | — | — |
| A, B, C, D | I-ppoi homing endonuclease | protein | 162 | 19% helix, 31% strand | Q94702 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains G, N, D, H, P, C, F, O, A, M, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 872 | 0.72 | 0.77 | 73 | empty |
| 2 | 136 | 0.67 | 0.89 | 28 | empty |
| 3 | 123 | 0.63 | 0.87 | 26 | empty |
| 4 | 272 | 0.59 | 0.79 | 32 | empty |
| 5 | 222 | 0.56 | 0.79 | 31 | empty |
Interfaces
26 interfaces between chains.
- A–B · 2530 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 2523 Ų buried · 37 hydrogen bonds · protein-protein
- N–D · 475 Ų buried · 19 hydrogen bonds · protein-nucleic
- O–A · 470 Ų buried · 14 hydrogen bonds · protein-nucleic
- P–C · 469 Ų buried · 16 hydrogen bonds · protein-nucleic
Compared structures
- 1EVW · L116A mutant of the homing endonuclease I-ppoi complexed to homing site DNA. · the same entry in another collection · chain C against C, 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 Q94702
- Elsewhere: RCSB PDB 1EVW · PDBe 1EVW · UniProt Q94702
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